From 0460e93f0832ed10316eed05a4d6f2ceb5b61922 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 16 Feb 2020 04:54:10 -0600
Subject: gn: ratspub: wrap with more referenced binaries

---
 gn/packages/ratspub.scm | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

(limited to 'gn')

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 29e1313..290b9e2 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -65,7 +65,10 @@
              (let ((out  (assoc-ref outputs "out"))
                    (path (getenv "PYTHONPATH")))
                (wrap-program (string-append out "/server.py")
-                 `("PATH" ":" prefix (,(dirname (which "edirect.pl"))))
+                 `("PATH" ":" prefix (,(dirname (which "edirect.pl"))
+                                      ,(dirname (which "dirname"))
+                                      ,(dirname (which "grep"))
+                                      ,(dirname (which "sed"))))
                  `("PYTHONPATH" ":" prefix (,path))))
              #t)))))
     (inputs
-- 
cgit v1.2.3


From bc065d21f3add434a4c5958ffe93383c2d848795 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 16 Feb 2020 04:56:41 -0600
Subject: gn: edirect-gn: Wrap more binaries

---
 gn/packages/bioinformatics.scm | 30 +++++++++++++-----------------
 1 file changed, 13 insertions(+), 17 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 8897752..66d4d2d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -427,20 +427,12 @@ reads.")
          ;       (let ((go (string-append (assoc-ref inputs "go") "/bin/go")))
          ;         (invoke go "build" "xtract.go"))))
             (add-after 'unpack 'patch-programs
-              (lambda* (#:key inputs #:allow-other-keys)
-                (let ((gzip (assoc-ref inputs "gzip")))
-                  (substitute* '("index-bioc"
-                                 "pm-index"
-                                 "pm-invert"
-                                 "pm-stash"
-                                 "rchive.go"
-                                 "run-ncbi-converter")
-                    (("gunzip") (string-append gzip "/bin/gunzip")))
-                  (substitute* (find-files "." "^e")
-                    (("exec perl") "exec"))
-                  (substitute* '("xtract" "rchive")
-                    ;; or add current directory to PATH
-                    ((".*PATH.*") "")))
+              (lambda _
+                (substitute* (find-files "." "^e")
+                  (("exec perl") "exec"))
+                (substitute* '("xtract" "rchive")
+                  ;; or add current directory to PATH
+                  ((".*PATH.*") ""))
                 #t))
             (replace 'install
               (lambda* (#:key inputs outputs #:allow-other-keys)
@@ -466,9 +458,13 @@ reads.")
                       (path (getenv "PERL5LIB")))
                   (for-each
                     (lambda (file)
-                      (wrap-program (string-append out "/bin/" file)
-                                    `("PERL5LIB" ":" prefix (,path))))
-                    '("edirect.pl" "asp-ls" "ftp-cp" "ftp-ls")))
+                      (wrap-program file
+                                    `("PERL5LIB" ":" prefix (,path)))
+                      (wrap-program file
+                                    `("PATH" ":" prefix (,(dirname (which "sed"))
+                                                         ,(dirname (which "gzip"))
+                                                         ,(dirname (which "uname"))))))
+                    (find-files out ".")))
                 #t))))))
     (inputs
      `(("gzip" ,gzip)
-- 
cgit v1.2.3


From 0bd3232df5340a9882c88804af6b4029f6c613c9 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 17 Feb 2020 00:57:32 -0600
Subject: gn: octave@3.4: Skip tests

---
 gn/packages/maths.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gn')

diff --git a/gn/packages/maths.scm b/gn/packages/maths.scm
index 9e15400..1c1c1ae 100644
--- a/gn/packages/maths.scm
+++ b/gn/packages/maths.scm
@@ -30,6 +30,7 @@
        ((#:configure-flags cf)
         `(cons "--enable-docs=no" ; docs fail to build
                ,cf))
+       ((#:tests? _ #f) #f) ; tests hang
        ((#:phases phases)
         `(modify-phases ,phases
            (add-after 'unpack 'patch-configure-script
-- 
cgit v1.2.3


From 9a16a60554a798a805ec27cfaaa2aa23c50483dd Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 17 Feb 2020 02:03:44 -0600
Subject: gn: Run BNW entirely inside a container

---
 gn/services/bnw-container.scm | 4 ----
 1 file changed, 4 deletions(-)

(limited to 'gn')

diff --git a/gn/services/bnw-container.scm b/gn/services/bnw-container.scm
index 8463a75..39da38d 100644
--- a/gn/services/bnw-container.scm
+++ b/gn/services/bnw-container.scm
@@ -21,10 +21,6 @@
   (match-lambda
     (($ <bnw-configuration> package deploy-directory port)
      #~(begin
-         (use-modules (guix build utils))
-         (when (directory-exists? #$deploy-directory)
-           ;; Not 'delete-file-recursively' because the directory might be empty.
-           (system* "rm" "-r" #$(string-append deploy-directory "/*")))
          (mkdir-p #$deploy-directory)
          (copy-recursively #$package #$deploy-directory)
          (invoke #$(file-append coreutils "/bin/chmod") "a+w"
-- 
cgit v1.2.3


From 1b33411fca0c3a059542525f5e317bfe00d8c060 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 17 Feb 2020 02:04:59 -0600
Subject: gn: bnw: Only use packaged javascript

---
 gn/packages/bnw.scm | 140 ++++++++++++++++++++++++++++++++++------------------
 1 file changed, 91 insertions(+), 49 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index 5c97eab..043077d 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -14,7 +14,7 @@
 
 (define-public bnw
   (let ((commit "eb6b002b924694808384f1a8d7c6d1121806ae04")
-        (revision "5"))
+        (revision "6"))
     (package
       (name "bnw")
       (version (git-version "1.22" revision commit)) ; June 28, 2019
@@ -86,59 +86,101 @@
                    (("rmdir ") (string-append (which "rmdir") " "))
                    (("wc ") (string-append (which "wc") " ")))
                #t)))
-           ;(add-after 'patch-source-shebangs 'replace-javascript
-           ;  (lambda* (#:key inputs #:allow-other-keys)
-           ;    (let (
-           ;          (jquery        (assoc-ref inputs "jquery"))
-           ;          (awesome       (assoc-ref inputs "awesome"))
-           ;          (cyto          (assoc-ref inputs "cytoscape"))
-           ;          (cyto2         (assoc-ref inputs "cytoscape-2"))
-           ;          (cs-dagre      (assoc-ref inputs "cyto-dagre"))
-           ;          (d3js          (assoc-ref inputs "d3js"))
-           ;          (d3js-multi    (assoc-ref inputs "d3js-multi"))
-           ;          (dagre         (assoc-ref inputs "dagre"))
-           ;          (lodash        (assoc-ref inputs "lodash"))
-           ;          (canvas-toblob (assoc-ref inputs "canvas-toblob"))
-           ;          (filesaver     (assoc-ref inputs "filesaver"))
-           ;          (panzoom       (assoc-ref inputs "panzoom"))
-           ;          (js-path "/share/genenetwork2/javascript/")
-           ;          )
-                 ;(substitute* "sourcecodes/layout_cyto.php"
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js")
-                 ;   (string-append cyto js-path "cytoscape/cytoscape.min.js"))
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/2.7.29/cytoscape.min.js")
-                 ;   (string-append cyto2 js-path "cytoscape/cytoscape.min.js"))
-                 ;  (("http://spades.bioinf.spbau.ru/~alla/graph_viewer/js/cytoscape-dagre.js")
-                 ;   (string-append cs-dagre js-path "cytoscape-dagre/cytoscape-dagre.js"))
-                 ;  (("https://unpkg.com/dagre@0.7.4/dist/dagre.js")
-                 ;   (string-append dagre js-path "dagre/dagre.js"))
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape.js-panzoom.css")
-                 ;   (string-append panzoom js-path "cytoscape-panzoom/cytoscape.js-panzoom.css"))
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape-panzoom.js")
-                 ;   (string-append panzoom js-path "cytoscape-panzoom/cytoscape-panzoom.js"))
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.0.3/css/font-awesome.css")
-                 ;   (string-append awesome "/share/web/font-awesome/css/font-awesome.css"))
-                 ;  (("https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js")
-                 ;   (string-append jquery "/share/web/jquery/jquery.min.js"))
-                 ;  (("https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.10/lodash.js")
-                 ;   (string-append lodash js-path "lodash/lodash.js")))
-                 ;(substitute* '("sourcecodes/layout_svg_wt.php"
-                 ;               "sourcecodes/layout_svg_no.php")
-                 ;  (("http://d3js.org/d3.v4.min.js")
-                 ;   (string-append d3js js-path "d3js/d3.min.js"))
-                 ;  (("http://d3js.org/d3-selection-multi.v1.js")
-                 ;   (string-append d3js-multi js-path "d3js-multi/d3-selection-multi.js"))
-                 ;  (("https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js")
-                 ;   (string-append canvas-toblob js-path "canvas-toBlob/canvas-toBlob.js"))
-                 ;  (("https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js")
-                 ;   (string-append filesaver js-path "filesaver/filesaver.js")))
-           ;      )
-           ;    #t))
+           (add-after 'patch-source-shebangs 'replace-javascript
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((jquery        (assoc-ref inputs "jquery"))
+                     (awesome       (assoc-ref inputs "awesome"))
+                     (cyto          (assoc-ref inputs "cytoscape"))
+                     (cyto2         (assoc-ref inputs "cytoscape-2"))
+                     (cs-dagre      (assoc-ref inputs "cyto-dagre"))
+                     (d3js          (assoc-ref inputs "d3js"))
+                     (d3js-multi    (assoc-ref inputs "d3js-multi"))
+                     (dagre         (assoc-ref inputs "dagre"))
+                     (lodash        (assoc-ref inputs "lodash"))
+                     (canvas-toblob (assoc-ref inputs "canvas-toblob"))
+                     (filesaver     (assoc-ref inputs "filesaver"))
+                     (panzoom       (assoc-ref inputs "panzoom"))
+                     (js-path "/share/genenetwork2/javascript/"))
+                 (substitute* "sourcecodes/layout_cyto.php"
+                   (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.7.1/cytoscape.min.js")
+                    "/javascript/cytoscape.min.js")
+                   (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape/2.7.29/cytoscape.min.js")
+                    "/javascript/cytoscape2.min.js")
+                   (("http://spades.bioinf.spbau.ru/~alla/graph_viewer/js/cytoscape-dagre.js")
+                    "/javascript/cytoscape-dagre.js")
+                   (("https://unpkg.com/dagre@0.7.4/dist/dagre.js")
+                    "/javascript/dagre.js")
+                   (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape.js-panzoom.css")
+                    "/javascript/cytoscape.js-panzoom.css")
+                   (("https://cdnjs.cloudflare.com/ajax/libs/cytoscape-panzoom/2.5.3/cytoscape-panzoom.js")
+                    "/javascript/cytoscape-panzoom.js")
+                   (("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.0.3/css/font-awesome.css")
+                    "/javascript/font-awesome.css")
+                   (("https://ajax.googleapis.com/ajax/libs/jquery/3.1.0/jquery.min.js")
+                    "/javascript/jquery.min.js")
+                   (("https://cdnjs.cloudflare.com/ajax/libs/lodash.js/4.17.10/lodash.js")
+                    "/javascript/lodash.js"))
+                 (substitute* '("sourcecodes/layout_svg_wt.php"
+                                "sourcecodes/layout_svg_no.php")
+                   (("http://d3js.org/d3.v4.min.js")
+                    "/javascript/d3.min.js")
+                   (("http://d3js.org/d3-selection-multi.v1.js")
+                    "/javascript/d3-selection-multi.js")
+                   (("https://cdn.rawgit.com/eligrey/canvas-toBlob.js/f1a01896135ab378aa5c0118eadd81da55e698d8/canvas-toBlob.js")
+                    "/javascript/canvas-toBlob.js")
+                   (("https://cdn.rawgit.com/eligrey/FileSaver.js/e9d941381475b5df8b7d7691013401e171014e89/FileSaver.min.js")
+                    "/javascript/filesaver.js")))
+               #t))
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((out (assoc-ref outputs "out")))
                  (copy-recursively "." out))
                #t))
+           (add-after 'install 'install-javascript-libraries
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let ((out (assoc-ref outputs "out"))
+                     (jquery        (assoc-ref inputs "jquery"))
+                     (awesome       (assoc-ref inputs "awesome"))
+                     (cyto          (assoc-ref inputs "cytoscape"))
+                     (cyto2         (assoc-ref inputs "cytoscape-2"))
+                     (cs-dagre      (assoc-ref inputs "cyto-dagre"))
+                     (d3js          (assoc-ref inputs "d3js"))
+                     (d3js-multi    (assoc-ref inputs "d3js-multi"))
+                     (dagre         (assoc-ref inputs "dagre"))
+                     (lodash        (assoc-ref inputs "lodash"))
+                     (canvas-toblob (assoc-ref inputs "canvas-toblob"))
+                     (filesaver     (assoc-ref inputs "filesaver"))
+                     (panzoom       (assoc-ref inputs "panzoom"))
+                     (js-path  "/share/genenetwork/javascript/")
+                     (js-path2 "/share/genenetwork2/javascript/"))
+                 (mkdir-p (string-append out "/javascript"))
+                 (symlink (string-append (string-append cyto2 js-path2 "cytoscape/cytoscape.min.js"))
+                          (string-append out "/javascript/cytoscape.min.js"))
+                 (symlink (string-append (string-append cyto js-path2 "cytoscape/cytoscape.min.js"))
+                          (string-append out "/javascript/cytoscape2.min.js"))
+                 (symlink (string-append cs-dagre js-path2 "cytoscape-dagre/cytoscape-dagre.js")
+                          (string-append out "/javascript/cytoscape-dagre.js"))
+                 (symlink (string-append dagre js-path2 "dagre/dagre.js")
+                          (string-append out "/javascript/dagre.js"))
+                 (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape.js-panzoom.css")
+                          (string-append out "/javascript/cytoscape.js-panzoom.css"))
+                 (symlink (string-append panzoom js-path2 "cytoscape-panzoom/cytoscape-panzoom.js")
+                          (string-append out "/javascript/cytoscape-panzoom.js"))
+                 (symlink (string-append awesome "/share/web/font-awesomecss/font-awesome.css")
+                          (string-append out "/javascript/font-awesome.css"))
+                 (symlink (string-append jquery "/share/web/jquery/jquery.min.js")
+                          (string-append out "/javascript/jquery.min.js"))
+                 (symlink (string-append lodash js-path2 "lodash/lodash.js")
+                          (string-append out "/javascript/lodash.js"))
+                 (symlink (string-append d3js js-path "d3js/d3.min.js")
+                          (string-append out "/javascript/d3.min.js"))
+                 (symlink (string-append d3js-multi js-path "d3js-multi/d3-selection-multi.js")
+                          (string-append out "/javascript/d3-selection-multi.js"))
+                 (symlink (string-append canvas-toblob js-path "canvas-toblob/canvas-toBlob.js")
+                          (string-append out "/javascript/canvas-toBlob.js"))
+                 (symlink (string-append filesaver js-path2 "filesaver/FileSaver.js")
+                          (string-append out "/javascript/filesaver.js"))
+               #t)))
            (add-after 'install 'make-files-executable
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((out (assoc-ref outputs "out")))
-- 
cgit v1.2.3


From a07cc9e17734383f2b305b1fc05a683500539383 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 17 Feb 2020 02:14:35 -0600
Subject: add archive-pubmed systemd service and timer

---
 gn/services/archive-pubmed.service | 13 +++++++++++++
 gn/services/archive-pubmed.timer   |  9 +++++++++
 2 files changed, 22 insertions(+)
 create mode 100644 gn/services/archive-pubmed.service
 create mode 100644 gn/services/archive-pubmed.timer

(limited to 'gn')

diff --git a/gn/services/archive-pubmed.service b/gn/services/archive-pubmed.service
new file mode 100644
index 0000000..fd00b71
--- /dev/null
+++ b/gn/services/archive-pubmed.service
@@ -0,0 +1,13 @@
+[Unit]
+Description=Download PubMed Archives
+After=network-online.target
+Wants=network-online.target
+AssertPathExists=/export2/PubMed
+
+[Service]
+ExecStart=/usr/local/guix-profiles/ratspub/bin/archive-pubmed
+Environment="EDIRECT_PUBMED_MASTER=/export2/PubMed" "PERL_LWP_SSL_CA_FILE=/etc/ssl/certs/ca-certificates.crt" "PATH=/usr/local/guix-profiles/ratspub/bin:/usr/sbin:/usr/bin:/sbin:/bin:/sbin:/usr/sbin"
+User=hchen
+
+[Install]
+WantedBy=multi-user.target
diff --git a/gn/services/archive-pubmed.timer b/gn/services/archive-pubmed.timer
new file mode 100644
index 0000000..4bb27ba
--- /dev/null
+++ b/gn/services/archive-pubmed.timer
@@ -0,0 +1,9 @@
+[Unit]
+Description=Daily PubMed downloads
+
+[Timer]
+OnBootSec=5h
+OnUnitInactiveSec=15h
+
+[Install]
+WantedBy=default.target
-- 
cgit v1.2.3


From ae659bb705d771be310c86c518d4712812aaafce Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 17 Feb 2020 02:21:04 -0600
Subject: gn: Update BNW service and README

---
 gn/services/bnw-README  | 4 ++--
 gn/services/bnw.service | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

(limited to 'gn')

diff --git a/gn/services/bnw-README b/gn/services/bnw-README
index ab7de53..d70b7fc 100644
--- a/gn/services/bnw-README
+++ b/gn/services/bnw-README
@@ -6,8 +6,8 @@ $ cd guix-bioinformatics && git pull
 # systemctl enable --now bnw.service
 
 for testing changes to the container, you'll want to do the following (or thereabouts):
-$ guix system container gn/services/GN1-container.scm --share=/home/bnw/server=/srv/http --network
-$ sudo -E $(guix system container gn/services/GN1-container.scm --share=/home/bnw/server=/srv/http --network)
+$ guix system container gn/servicebnwN1-container.scm --network
+$ sudo -E $(guix system container gn/services/bnw-container.scm --network)
 
 for running the service:
 see included bnw.service
diff --git a/gn/services/bnw.service b/gn/services/bnw.service
index 5ba8f3f..6ac99a1 100644
--- a/gn/services/bnw.service
+++ b/gn/services/bnw.service
@@ -3,7 +3,7 @@ Description=BNW web server
 Wants=guix-daemon.service
 
 [Service]
-Environment="BNW_COMMAND=$(/bin/su -l bnw -c '/var/guix/profiles/per-user/bnw/current-guix/bin/guix system container /home/bnw/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/bnw/server=/srv/http --share=/home/bnw/server/var-log=/var/log --network')"
+Environment="BNW_COMMAND=$(/bin/su -l bnw -c '/var/guix/profiles/per-user/bnw/current-guix/bin/guix system container /home/bnw/guix-bioinformatics/gn/services/bnw-container.scm --share=/home/bnw/server/var-log=/var/log --network')"
 ExecStart=/bin/bash -c '${BNW_COMMAND}'
 
 [Install]
-- 
cgit v1.2.3


From f5d94e1aba06f21fbaa3224b8942d5714405407c Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 17 Feb 2020 02:24:59 -0600
Subject: fix typo

---
 gn/services/genenetwork.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gn')

diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm
index 0978cd2..5acbcea 100644
--- a/gn/services/genenetwork.scm
+++ b/gn/services/genenetwork.scm
@@ -38,7 +38,7 @@
                              (config
                                (httpd-config-file
                                  (server-name "www.genenetwork.org")
-                                 (document-root (file-append genenetwork "/web"))
+                                 (document-root (file-append genenetwork1 "/web"))
                                  (listen '("8811"))
                                  (modules (cons*
                                             (httpd-module
-- 
cgit v1.2.3


From 5656ce244f8ff8af0347c7206451e88bf1769a5d Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 17 Feb 2020 02:27:51 -0600
Subject: fix typo

---
 gn/services/genenetwork.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gn')

diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm
index 5acbcea..516c124 100644
--- a/gn/services/genenetwork.scm
+++ b/gn/services/genenetwork.scm
@@ -46,8 +46,8 @@
                                               (file (file-append mod-python "/modules/mod_python.so")))
                                             %default-httpd-modules))
                                  (extra-config (list "\
-PythonPath \"sys.path+['" %mod-python-path "', '" (file-append genenetwork "/web/webqtl") "']\"
-<Directory " (file-append genenetwork "/web/webqtl") ">
+PythonPath \"sys.path+['" %mod-python-path "', '" (file-append genenetwork1 "/web/webqtl") "']\"
+<Directory " (file-append genenetwork1 "/web/webqtl") ">
   SetHandler python-program
   PythonHandler mod_python.publisher
   PythonAutoReload Off
-- 
cgit v1.2.3


From dce1ae9dbfe7c33dcac7f64682eb9368b6480b6d Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 18 Feb 2020 13:32:09 +0200
Subject: gn: Update edirect-gn to match upstream update.

---
 gn/packages/bioinformatics.scm | 31 ++++++++++++++++++++-----------
 1 file changed, 20 insertions(+), 11 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 66d4d2d..4cb8c7c 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -426,6 +426,15 @@ reads.")
          ;     (lambda* (#:key inputs #:allow-other-keys)
          ;       (let ((go (string-append (assoc-ref inputs "go") "/bin/go")))
          ;         (invoke go "build" "xtract.go"))))
+            (add-after 'unpack 'unpack-binaries
+              (lambda* (#:key inputs #:allow-other-keys)
+                (let ((gzip (assoc-ref inputs "gzip"))
+                      (xtract (assoc-ref inputs "xtract.Linux"))
+                      (rchive (assoc-ref inputs "rchive.Linux")))
+                  (copy-file xtract "xtract.Linux.gz")
+                  (copy-file rchive "rchive.Linux.gz")
+                  (invoke (string-append gzip "/bin/gzip") "xtract.Linux.gz" "-dfv")
+                  (invoke (string-append gzip "/bin/gzip") "rchive.Linux.gz" "-dfv"))))
             (add-after 'unpack 'patch-programs
               (lambda _
                 (substitute* (find-files "." "^e")
@@ -435,10 +444,8 @@ reads.")
                   ((".*PATH.*") ""))
                 #t))
             (replace 'install
-              (lambda* (#:key inputs outputs #:allow-other-keys)
-                (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
-                      (xtract.linux (assoc-ref inputs "xtract.Linux"))
-                      (rchive.linux (assoc-ref inputs "rchive.Linux")))
+              (lambda* (#:key outputs #:allow-other-keys)
+                (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
                   (for-each
                     (lambda (file)
                       (install-file file bin))
@@ -446,8 +453,8 @@ reads.")
                       "edirect.pl" "efetch" "epost" "esearch" "fetch-pubmed"
                       "ftp-cp" "ftp-ls" "has-asp" "pm-prepare" "pm-refresh"
                       "pm-stash" "rchive" "xtract"))
-                  (copy-file xtract.linux (string-append bin "/xtract.Linux"))
-                  (copy-file rchive.linux (string-append bin "/rchive.Linux"))
+                  (install-file "xtract.Linux" bin)
+                  (install-file "rchive.Linux" bin)
                   (chmod (string-append bin "/xtract.Linux") #o555)
                   (chmod (string-append bin "/rchive.Linux") #o555))
                 #t))
@@ -475,19 +482,21 @@ reads.")
        ("xtract.Linux"
         ,(origin
            (method url-fetch)
-           (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
-                               "/xtract.Linux")) ;; March 10, 2016
+           (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
+                               "/versions/" (package-version edirect)
+                               "/xtract.Linux.gz"))
            (sha256
             (base32
-             "15yhhh8kfipk12rhzabap81ys8wgj0khn0mp8p7zwqhq028fwj0l"))))
+             "1idzynn446qqjx2wv4jjgsx6cp349d4jy8g9z4gsg9l6sn5dhx53"))))
        ("rchive.Linux"
         ,(origin
            (method url-fetch)
            (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
-                               "/rchive.Linux")) ;; November 14, 2017
+                               "/versions/" (package-version edirect)
+                               "/rchive.Linux.gz"))
            (sha256
             (base32
-             "0hl8zj1md9xbmaj0pv99rjyisw8w74rirw97xwqk47dz8v8ml338"))))))
+             "1p65hifv5d6nxg01vjwgy2nw49nssd822a8aj8jv412mhzj95ihv"))))))
     (native-search-paths
      ;; Ideally this should be set for LWP somewhere.
      (list (search-path-specification
-- 
cgit v1.2.3


From 91e66ebbd325ba32635d1145b0402f6ab0aaeb28 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 3 Mar 2020 01:31:26 -0600
Subject: WIP: incomplete update to singlecellrshiny.

---
 gn/packages/bioinformatics.scm | 29 +++++++++++++++++++++++++----
 1 file changed, 25 insertions(+), 4 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 4cb8c7c..6774df5 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -885,15 +885,19 @@ interest, and this app can provide values and figures for applicants to use.")
                  (app       (string-append out "/bin/" ,name))
                  (Rbin      (string-append (assoc-ref %build-inputs "r-min")
                                            "/bin/Rscript"))
+                 (top1001   (assoc-ref %build-inputs "RobTop1001.csv"))
+                 (celltypes (assoc-ref %build-inputs "CellTypes_RGC_Master_08Dec2018.csv"))
                  (source    (assoc-ref %build-inputs "source")))
             (copy-recursively source targetdir)
+            (copy-file celltypes (string-append targetdir "/CellTypes_RGC_Master_08Dec2018.csv"))
+            (copy-file top1001 (string-append targetdir "/RobTop1001.csv"))
             (substitute* (string-append targetdir "/global.R")
               (("800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv")
                "shinyRappToyDataset_SiamakPlay.csv")
               ;; Comment out the two unreferenced files for now
-              (("^rgc.*") "")
-              ;(("CellTypes_RGC_Master_08Dec2018.csv") "")
-              ;(("RobTop1001.csv") "")
+              ;(("^rgc.*") "")
+              ;(("CellTypes_RGC_Master_08Dec2018.csv") celltypes)
+              ;(("RobTop1001.csv") top1001)
               )
             (mkdir-p (string-append out "/bin"))
             (call-with-output-file app
@@ -906,7 +910,24 @@ runApp(launch.browser=0, port=4208)~%\n"
                 Rbin targetdir)))
             (chmod app #o555)
             #t))))
-     (native-inputs `(("source" ,source)))
+     (native-inputs
+      `(
+        ("source" ,source)
+        ("RobTop1001.csv"
+         ,(origin
+            (method url-fetch)
+            (uri "https://archive.org/download/celltypesrgcmaster08dec2018/RobTop1001.csv")
+            (file-name "RobTop1001.csv")
+            (sha256
+             (base32 "0pa73kc1p8417sjvvvhp9xsbh2h8g7h85pnmm16mnv4wjalhq0gn"))))
+        ("CellTypes_RGC_Master_08Dec2018.csv"
+         ,(origin
+            (method url-fetch)
+            (uri "https://archive.org/download/celltypesrgcmaster08dec2018/CellTypes_RGC_Master_08Dec2018.csv")
+            (file-name "CellTypes_RGC_Master_08Dec2018.csv")
+            (sha256
+             (base32 "0y411968np1f5g21iym9xc9yj5c1jsn94rpkwkxh9pw2z43gvghn"))))
+        ))
      (inputs
       `(("r-min" ,r-minimal)))
      (propagated-inputs
-- 
cgit v1.2.3


From 3c3c3e830ccc4fe56f6db77e770bd533c7bdc96a Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Wed, 4 Mar 2020 04:36:21 -0600
Subject: WIP: singlecellrshiny

---
 gn/packages/bioinformatics.scm | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 6774df5..94e7010 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -14,6 +14,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
+  #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages boost)
   #:use-module (gnu packages check)
@@ -861,19 +862,19 @@ interest, and this app can provide values and figures for applicants to use.")
         (license license:gpl3))))
 
 (define-public singlecellrshiny
-  (let ((commit "8061dcb477ba355de77d3e4fd3a15cf3267b56af")
-        (revision "1"))
+  (let ((commit "bdca74f4819d11e8fe7b15d9ab91b853f6542f7a")
+        (revision "2"))
     (package
      (name "singlecellrshiny")
      (version (git-version "0.0.0" revision commit))
      (source (origin
        (method git-fetch)
        (uri (git-reference
-              (url "https://github.com/syousefi/singleCellRshiny.git")
+              (url "https://github.com/genenetwork/singleCellRshiny")
               (commit commit)))
        (file-name (git-file-name name version))
        (sha256
-        (base32 "1pd8a9jx6ijjggsifvq66madx31h29rah5pmz4kdzfzb4fskpqz1"))))
+        (base32 "1rxj933s9p9r7358vnp15f7ag6c0j65r4hgr8kyirfhmp1i8xdlw"))))
      (build-system trivial-build-system)
      (arguments
       `(#:modules ((guix build utils))
@@ -891,13 +892,20 @@ interest, and this app can provide values and figures for applicants to use.")
             (copy-recursively source targetdir)
             (copy-file celltypes (string-append targetdir "/CellTypes_RGC_Master_08Dec2018.csv"))
             (copy-file top1001 (string-append targetdir "/RobTop1001.csv"))
+            (substitute* (string-append targetdir "/app.R")
+            ;  (("install.package.*") "")
+              ;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch
+              (("library\\(DT\\)") "library(DT)\nlibrary(multtest)")
+              )
             (substitute* (string-append targetdir "/global.R")
               (("800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv")
                "shinyRappToyDataset_SiamakPlay.csv")
               ;; Comment out the two unreferenced files for now
               ;(("^rgc.*") "")
-              ;(("CellTypes_RGC_Master_08Dec2018.csv") celltypes)
-              ;(("RobTop1001.csv") top1001)
+              (("CellTypes_RGC_Master_08Dec2018.csv") celltypes)
+              (("RobTop1001.csv") top1001)
+              ;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch
+              (("dim\\(sc.object.1") "dim(sc.object")
               )
             (mkdir-p (string-append out "/bin"))
             (call-with-output-file app
@@ -933,6 +941,7 @@ runApp(launch.browser=0, port=4208)~%\n"
      (propagated-inputs
       `(("r" ,r)
         ("r-dt" ,r-dt)
+        ("r-multtest" ,r-multtest)
         ("r-seurat" ,r-seurat)
         ("r-shiny" ,r-shiny)))
      (home-page "http://rn6err.opar.io/")
@@ -940,7 +949,7 @@ runApp(launch.browser=0, port=4208)~%\n"
      (description
       "This is the R-Shiny programs to run some basic single cell RNA sequencing
 (scRNA-seq) data analysis.")
-     (license license:gpl3))))
+     (license #f))))
 
 (define-public seqwish
   (package
-- 
cgit v1.2.3


From d3d71158cb0cd1499970a62c3800dc64ec84ecbc Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 5 Mar 2020 08:39:11 -0600
Subject: gn: singlecellrshiny is ready

---
 gn/packages/bioinformatics.scm | 36 ++++++++++++++++--------------------
 1 file changed, 16 insertions(+), 20 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 94e7010..40a992a 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -863,7 +863,7 @@ interest, and this app can provide values and figures for applicants to use.")
 
 (define-public singlecellrshiny
   (let ((commit "bdca74f4819d11e8fe7b15d9ab91b853f6542f7a")
-        (revision "2"))
+        (revision "3"))
     (package
      (name "singlecellrshiny")
      (version (git-version "0.0.0" revision commit))
@@ -888,25 +888,18 @@ interest, and this app can provide values and figures for applicants to use.")
                                            "/bin/Rscript"))
                  (top1001   (assoc-ref %build-inputs "RobTop1001.csv"))
                  (celltypes (assoc-ref %build-inputs "CellTypes_RGC_Master_08Dec2018.csv"))
+                 (800-H1    (assoc-ref %build-inputs "800-H1-H20-RNA-Seq.csv"))
                  (source    (assoc-ref %build-inputs "source")))
             (copy-recursively source targetdir)
-            (copy-file celltypes (string-append targetdir "/CellTypes_RGC_Master_08Dec2018.csv"))
-            (copy-file top1001 (string-append targetdir "/RobTop1001.csv"))
             (substitute* (string-append targetdir "/app.R")
-            ;  (("install.package.*") "")
               ;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch
-              (("library\\(DT\\)") "library(DT)\nlibrary(multtest)")
-              )
+              (("library\\(DT\\)") "library(DT)\nlibrary(multtest)"))
             (substitute* (string-append targetdir "/global.R")
-              (("800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv")
-               "shinyRappToyDataset_SiamakPlay.csv")
-              ;; Comment out the two unreferenced files for now
-              ;(("^rgc.*") "")
+              (("800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv") 800-H1)
               (("CellTypes_RGC_Master_08Dec2018.csv") celltypes)
               (("RobTop1001.csv") top1001)
               ;; As seen in https://github.com/genenetwork/singleCellRshiny/commit/6b2a344dd0d02f65228ad8c350bac0ced5850d05.patch
-              (("dim\\(sc.object.1") "dim(sc.object")
-              )
+              (("dim\\(sc.object.1") "dim(sc.object"))
             (mkdir-p (string-append out "/bin"))
             (call-with-output-file app
               (lambda (port)
@@ -918,9 +911,8 @@ runApp(launch.browser=0, port=4208)~%\n"
                 Rbin targetdir)))
             (chmod app #o555)
             #t))))
-     (native-inputs
-      `(
-        ("source" ,source)
+     (inputs
+      `(("r-min" ,r-minimal)
         ("RobTop1001.csv"
          ,(origin
             (method url-fetch)
@@ -935,21 +927,25 @@ runApp(launch.browser=0, port=4208)~%\n"
             (file-name "CellTypes_RGC_Master_08Dec2018.csv")
             (sha256
              (base32 "0y411968np1f5g21iym9xc9yj5c1jsn94rpkwkxh9pw2z43gvghn"))))
-        ))
-     (inputs
-      `(("r-min" ,r-minimal)))
+        ("800-H1-H20-RNA-Seq.csv"
+         ,(origin
+            (method url-fetch)
+            (uri "https://archive.org/download/celltypesrgcmaster08dec2018/800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv")
+            (file-name "800-H1-H20-RNA-Seq-SingleCell-Retina-OMRF-03-29-19_FPKM_v2_SiamakPlay.csv")
+            (sha256
+             (base32 "1b1y4lfs8drypm04i1rypbmk67rdqgs27nfh05pwnv3sja2nanam"))))))
      (propagated-inputs
       `(("r" ,r)
         ("r-dt" ,r-dt)
         ("r-multtest" ,r-multtest)
         ("r-seurat" ,r-seurat)
         ("r-shiny" ,r-shiny)))
-     (home-page "http://rn6err.opar.io/")
+     (home-page "")
      (synopsis "RNA sequencing data analysis")
      (description
       "This is the R-Shiny programs to run some basic single cell RNA sequencing
 (scRNA-seq) data analysis.")
-     (license #f))))
+     (license license:agpl3))))
 
 (define-public seqwish
   (package
-- 
cgit v1.2.3


From 9f6b35cac5aa37bf3568b8525f17542d7e471eb6 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Wed, 11 Mar 2020 03:12:40 -0500
Subject: gn: singlecellrshiny: Update home-page.

---
 gn/packages/bioinformatics.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 40a992a..7e7f94d 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -940,7 +940,7 @@ runApp(launch.browser=0, port=4208)~%\n"
         ("r-multtest" ,r-multtest)
         ("r-seurat" ,r-seurat)
         ("r-shiny" ,r-shiny)))
-     (home-page "")
+     (home-page "http://singlecell.opar.io/")
      (synopsis "RNA sequencing data analysis")
      (description
       "This is the R-Shiny programs to run some basic single cell RNA sequencing
-- 
cgit v1.2.3


From 99cbd15b00a71787257baaed86c1a3a0e23df137 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 12 Mar 2020 02:24:05 -0500
Subject: gn: Add grocsvs and dependencies

---
 gn/packages/bioinformatics.scm |  40 ++++++++++++
 gn/packages/python.scm         | 135 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 175 insertions(+)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 7e7f94d..177308b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -14,6 +14,7 @@
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
+  #:use-module (gn packages python)
   #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages boost)
@@ -1224,3 +1225,42 @@ here}.")
     (synopsis "Efficient sequence alignment of full genomes")
     (description "MUMmer is a versatil alignment tool for DNA and protein sequences.")
     (license license:artistic2.0)))
+
+(define-public grocsvs
+  (let ((commit "ecd956a65093a0b2c41849050e4512d46fecea5d")
+        (revision "1"))
+    (package
+      (name "grocsvs")
+      (version (git-version "0.2.6.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/grocsvs/grocsvs")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "14505725gr7qxc17cxxf0k6lzcwmgi64pija4mwf29aw70qn35cc"))))
+      (build-system python-build-system)
+      (arguments
+       `(#:python ,python-2))   ; Only python-2 supported.
+      (inputs
+       `(("python2-admiral" ,python2-admiral)
+         ("python2-h5py" ,python2-h5py)
+         ("python2-ipython-cluster-helper" ,python2-ipython-cluster-helper)
+         ("python2-networkx" ,python2-networkx)
+         ("python2-psutil" ,python2-psutil)
+         ("python2-pandas" ,python2-pandas)
+         ("python2-pybedtools" ,python2-pybedtools)
+         ("python2-pyfaidx" ,python2-pyfaidx)
+         ("python2-pygraphviz" ,python2-pygraphviz)
+         ("python2-pysam" ,python2-pysam)
+         ("python2-scipy" ,python2-scipy)))
+      (home-page "https://github.com/grocsvs/grocsvs")
+      (synopsis "Genome-wide reconstruction of complex structural variants")
+      (description
+       "@dfn{Genome-wide Reconstruction of Complex Structural Variants}
+(GROC-SVs), is a software pipeline for identifying large-scale structural
+variants, performing sequence assembly at the breakpoints, and reconstructing
+the complex structural variants using the long-fragment information from the
+10x Genomics platform.")
+      (license license:expat))))
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 60558a2..8493698 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -3,6 +3,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages attr)
   #:use-module (gnu packages base)
+  #:use-module (gnu packages bioinformatics)
   #:use-module (gnu packages check)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages databases)
@@ -1094,3 +1095,137 @@ spreadsheets without the need for COM objects.")
     (synopsis "")
     (description "")
     (license license:bsd-4)))
+
+(define-public python-ipython-cluster-helper
+  (package
+    (name "python-ipython-cluster-helper")
+    (version "0.6.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "ipython-cluster-helper" version))
+        (sha256
+         (base32
+          "1l6mlwxlkxpbvawfwk6qffich7ahg9hq2bxfissgz6144p3k4arj"))
+        (modules '((guix build utils)))
+        (snippet
+         '(begin (substitute* "requirements.txt"
+                   (("ipython.*") "ipython\n"))
+                 #t))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f      ; Test suite can't find IPython.
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
+             (if tests?
+               (begin
+                 (setenv "HOME" (getcwd))
+                 (add-installed-pythonpath inputs outputs)
+                 (invoke "python" "example/example.py" "--local"))
+               #t))))))
+    (propagated-inputs
+     `(("python-ipyparallel" ,python-ipyparallel)
+       ("python-ipython" ,python-ipython)
+       ("python-netifaces" ,python-netifaces)
+       ("python-pyzmq" ,python-pyzmq)
+       ("python-setuptools" ,python-setuptools)
+       ("python-six" ,python-six)))
+    (home-page "https://github.com/roryk/ipython-cluster-helper")
+    (synopsis
+     "Simplify IPython cluster start up and use for multiple schedulers")
+    (description
+     "@code{ipython-cluster-helper} creates a throwaway parallel IPython
+profile, launches a cluster and returns a view.  On program exit it shuts the
+cluster down and deletes the throwaway profile.")
+    (license license:expat)))
+
+(define-public python2-ipython-cluster-helper
+  (package-with-python2 python-ipython-cluster-helper))
+
+(define-public python-ipyparallel
+  (package
+    (name "python-ipyparallel")
+    (version "6.2.4")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "ipyparallel" version))
+        (sha256
+         (base32
+          "0rf0dbpxf5z82bw8lsjj45r3wdd4wc74anz4wiiaf2rbjqlb1ivn"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f ; RuntimeError: IO Loop failed to start
+       #:phases
+       (modify-phases %standard-phases
+         (add-before 'check 'prepare-for-tests
+           (lambda _
+             (setenv "HOME" (getcwd))
+             #t)))))
+    (propagated-inputs
+     `(("python-dateutil" ,python-dateutil)
+       ("python-decorator" ,python-decorator)
+       ("python-ipykernel" ,python-ipykernel)
+       ("python-ipython" ,python-ipython)
+       ("python-ipython-genutils" ,python-ipython-genutils)
+       ("python-jupyter-client" ,python-jupyter-client)
+       ("python-pyzmq" ,python-pyzmq)
+       ("python-tornado" ,python-tornado)
+       ("python-traitlets" ,python-traitlets)))
+    (native-inputs
+     `(("python-ipython" ,python-ipython)
+       ("python-mock" ,python-mock)
+       ("python-nose" ,python-nose)
+       ("python-pytest" ,python-pytest)
+       ("python-pytest-cov" ,python-pytest-cov)
+       ("python-testpath" ,python-testpath)))
+    (home-page "https://ipython.org/")
+    (synopsis "Interactive Parallel Computing with IPython")
+    (description
+     "@code{ipyparallel} is a Python package and collection of CLI scripts for
+controlling clusters for Jupyter.  @code{ipyparallel} contains the following
+CLI scripts:
+@enumerate
+@item ipcluster - start/stop a cluster
+@item ipcontroller - start a scheduler
+@item ipengine - start an engine
+@end enumerate")
+    (license license:bsd-3)))
+
+(define-public python2-ipyparallel
+  (let ((ipyparallel (package-with-python2 python-ipyparallel)))
+    (package
+      (inherit ipyparallel)
+      (propagated-inputs
+       `(("python2-futures" ,python2-futures)
+         ,@(package-propagated-inputs ipyparallel))))))
+
+(define-public python2-pyfaidx
+  (package-with-python2 python-pyfaidx))
+
+(define-public python-admiral
+  (package
+    (name "python-admiral")
+    (version "0.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "admiral" version))
+        (sha256
+         (base32
+          "1b2zjgyz94ld5wr7s4cm4x5sxijx3w0dmd7r2cq1s8iqjzz6rd1x"))))
+    (build-system python-build-system)
+    (arguments '(#:tests? #f))      ; No tests
+    (propagated-inputs
+     `(("python-humanfriendly" ,python-humanfriendly)))
+    (home-page "https://github.com/nspies/admiral")
+    (synopsis
+     "Simple python high-performance computing cluster batch submission")
+    (description
+     "Simple python high-performance computing cluster batch submission.")
+    (license #f)))      ; No license in repository.
+
+(define-public python2-admiral
+  (package-with-python2 python-admiral))
-- 
cgit v1.2.3


From 165e12f94388ee02f7924c39681ffacb81d23f68 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 12 Mar 2020 03:13:23 -0500
Subject: gn: Add missing module import.

---
 gn/packages/bioinformatics.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 177308b..86e2657 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -24,6 +24,7 @@
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages graphviz)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages jemalloc)
   #:use-module (gnu packages maths)
-- 
cgit v1.2.3


From 7e7a8a4c59ba52bea1ecd285361dae89cf29376b Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 12 Mar 2020 05:46:04 -0500
Subject: gn: edirect-gn: Build go packages from source.

---
 gn/packages/bioinformatics.scm |  56 +++++++++
 gn/packages/golang.scm         | 268 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 324 insertions(+)
 create mode 100644 gn/packages/golang.scm

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 86e2657..6a38499 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -10,10 +10,12 @@
   #:use-module (guix build-system ant)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
+  #:use-module (guix build-system go)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
+  #:use-module (gn packages golang)
   #:use-module (gn packages python)
   #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages bioinformatics)
@@ -24,6 +26,7 @@
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
+  #:use-module (gnu packages golang)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages jemalloc)
@@ -510,6 +513,59 @@ reads.")
     ;; Due to the precompiled binaries we download:
     (supported-systems '("x86_64-linux"))))
 
+(define-public edirect-go-programs
+  (package
+    (inherit edirect)
+    (name "edirect-go-programs")
+    (build-system go-build-system)
+    (arguments
+     `(#:install-source? #f
+       #:tests? #f      ; No tests.
+       #:import-path "ncbi.nlm.nih.gov/entrez/edirect"
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'replace-go-dependency
+           ;; This go library does not have any license.
+           ;; TODO: This should move to a source snippet.
+           (lambda* (#:key import-path #:allow-other-keys)
+             (with-directory-excursion (string-append "src/" import-path)
+               (substitute* "rchive.go"
+                 (("github.com/fiam/gounidecode/unidecode")
+                  "golang.org/rainycape/unidecode"))
+               #t)))
+         (replace 'build
+           (lambda* (#:key import-path #:allow-other-keys)
+             (with-directory-excursion (string-append "src/" import-path)
+               (invoke "go" "build" "-v" "-x" "j2x.go")
+               (invoke "go" "build" "-v" "-x" "t2x.go")
+               (invoke "go" "build" "-v" "-x" "-o"
+                       "xtract.Linux" "xtract.go" "common.go")
+               (invoke "go" "build" "-v" "-x" "-o"
+                       "rchive.Linux" "rchive.go" "common.go")
+               (invoke "go" "build" "-v" "-x" "-o" "symbols.Linux" "s2p.go"))))
+         (replace 'install
+           (lambda* (#:key outputs import-path #:allow-other-keys)
+             (let ((dest    (string-append (assoc-ref outputs "out") "/bin"))
+                   (source  (string-append "src/" import-path "/")))
+               (for-each (lambda (file)
+                           (format #t "installing ~a~%" file)
+                           (install-file (string-append source file) dest))
+                         '("j2x" "t2x" "symbols.Linux" "xtract.Linux" "rchive.Linux"))
+               #t))))))
+    (native-inputs '())
+    (propagated-inputs '())
+    (inputs
+     `(("go-github-com-fatih-color" ,go-github-com-fatih-color)
+       ("go-github-com-fogleman-gg" ,go-github-com-fogleman-gg)
+       ("go-github-com-gedex-inflector" ,go-github-com-gedex-inflector)
+       ("go-github-com-golang-freetype" ,go-github-com-golang-freetype)
+       ("go-github-com-klauspost-cpuid" ,go-github-com-klauspost-cpuid)
+       ("go-github-com-pbnjay-memory" ,go-github-com-pbnjay-memory)
+       ("go-github-com-surgebase-porter2" ,go-github-com-surgebase-porter2)
+       ("go-golang-org-rainycape-unidecode" ,go-golang-org-rainycape-unidecode)
+       ("go-golang-org-x-image" ,go-golang-org-x-image)
+       ("go-golang-org-x-text" ,go-golang-org-x-text)))))
+
 ;; TODO: Unbundle zlib, bamtools, tclap
 (define-public sniffles
   (package
diff --git a/gn/packages/golang.scm b/gn/packages/golang.scm
new file mode 100644
index 0000000..56eed66
--- /dev/null
+++ b/gn/packages/golang.scm
@@ -0,0 +1,268 @@
+(define-module (gn packages golang)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix git-download)
+  #:use-module (guix packages)
+  #:use-module (guix utils)
+  #:use-module (guix build-system go)
+  #:use-module (gnu packages golang)
+  )
+
+(define-public go-golang-org-x-image
+  (let ((commit "58c23975cae11f062d4b3b0c143fe248faac195d")
+        (revision "1"))
+    (package
+      (name "go-golang-org-x-image")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://go.googlesource.com/image")
+                       (commit commit)))
+                (file-name (string-append "go.googlesource.com-image-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "0i2p2girc1sfcic6xs6vrq0fp3szfx057xppksb67kliywjjrm5x"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "golang.org/x/image"
+         ; Source-only package
+         #:tests? #f
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'build))))
+      (home-page "https://go.googlesource.com/image")
+      (synopsis "Supplemental Go image libraries")
+      (description "This package provides supplemental Go libraries for image
+processing.")
+      (license license:bsd-3))))
+
+(define-public go-github-com-fiam-gounidecode
+  (let ((commit "311ebb7422d3ff70cc1d064c5a297520ff5f304a")
+        (revision "1"))
+    (package
+      (name "go-github-com-fiam-gounidecode")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/fiam/gounidecode")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-fiam-gounidecode-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "107c2qnlgl9d55pww3kh3x5m5pqw7ijzzqbpsrpxnzn5jls44xbs"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:unpack-path "github.com/fiam/gounidecode"
+         #:import-path "github.com/fiam/gounidecode/unidecode"))
+      (home-page "https://github.com/fiam/gounidecode/")
+      (synopsis "Unicode transliterator for Go")
+      (description "Unicode transliterator for Go.")
+      (license #f))))       ; No license listed.
+
+(define-public go-golang-org-rainycape-unidecode
+  (let ((commit "cb7f23ec59bec0d61b19c56cd88cee3d0cc1870c")
+        (revision "1"))
+    (package
+      (name "go-golang-org-rainycape-unidecode")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/rainycape/unidecode")
+                       (commit commit)))
+                (file-name (string-append "go-golang-org-rainycape-unidecode-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "1wvzdijd640blwkgmw6h09frkfa04kcpdq87n2zh2ymj1dzla5v5"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "golang.org/rainycape/unidecode"))
+      (home-page "https://github.com/rainycape/unidecode")
+      (synopsis "Unicode transliterator in Golang")
+      (description "Unicode transliterator in Golang - Replaces non-ASCII
+characters with their ASCII approximations.")
+      (license license:asl2.0))))
+
+(define-public go-github-com-golang-freetype
+  (let ((commit "e2365dfdc4a05e4b8299a783240d4a7d5a65d4e4")
+        (revision "1"))
+    (package
+      (name "go-github-com-golang-freetype")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/golang/freetype")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-golang-freetype-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "194w3djc6fv1rgcjqds085b9fq074panc5vw582bcb8dbfzsrqxc"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/golang/freetype"))
+      (propagated-inputs
+       `(("go-golang-org-x-image" ,go-golang-org-x-image)))
+      (home-page "https://github.com/golang/freetype")
+      (synopsis "Freetype font rasterizer in the Go programming language")
+      (description "The Freetype font rasterizer in the Go programming language.")
+      (license (list license:freetype
+                     license:gpl2+)))))
+
+(define-public go-github-com-fogleman-gg
+  (package
+    (name "go-github-com-fogleman-gg")
+    (version "1.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/fogleman/gg")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1nkldjghbqnzj2djfaxhiv35kk341xhcrj9m2dwq65v684iqkk8n"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:tests? #f      ; Issue with test flags.
+       #:import-path "github.com/fogleman/gg"))
+    (propagated-inputs
+     `(("go-github-com-golang-freetype" ,go-github-com-golang-freetype)))
+    (home-page "https://github.com/fogleman/gg")
+    (synopsis "2D rendering in Go")
+    (description "@code{gg} is a library for rendering 2D graphics in pure Go.")
+    (license license:expat)))
+
+(define-public go-github-com-gedex-inflector
+  (let ((commit "16278e9db8130ac7ec405dc174cfb94344f16325")
+        (revision "1"))
+    (package
+      (name "go-github-com-gedex-inflector")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/gedex/inflector")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-gedex-inflector-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "05hjqw1m71vww4914d9h6nqa9jw3lgjzwsy7qaffl02s2lh1amks"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/gedex/inflector"))
+      (home-page "https://github.com/gedex/inflector")
+      (synopsis "Go library that pluralizes and singularizes English nouns")
+      (description "Go library that pluralizes and singularizes English nouns.")
+      (license license:bsd-2))))
+
+(define-public go-github-com-klauspost-cpuid
+  (package
+    (name "go-github-com-klauspost-cpuid")
+    (version "1.2.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/klauspost/cpuid")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1s510210wdj5dkamii1qrk7v87k4qpdcrrjzflp5ha9iscw6b06l"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/klauspost/cpuid"))
+    (home-page "https://github.com/klauspost/cpuid")
+    (synopsis "CPU feature identification for Go")
+    (description "@code{cpuid} provides information about the CPU running the
+current program.  CPU features are detected on startup, and kept for fast access
+through the life of the application. Currently x86 / x64 (AMD64) is supported,
+and no external C (cgo) code is used, which should make the library very eas
+to use.")
+    (license license:expat)))
+
+(define-public go-github-com-pbnjay-memory
+  (let ((commit "974d429e7ae40c89e7dcd41cfcc22a0bfbe42510")
+        (revision "1"))
+    (package
+      (name "go-github-com-pbnjay-memory")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/pbnjay/memory")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-pbnjay-memory-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "0kazg5psdn90pqadrzma5chdwh0l2by9z31sspr47gx93fhjmkkq"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/pbnjay/memory"))
+      (home-page "https://github.com/gedex/inflector")
+      (synopsis "Go library to report total system memory")
+      (description "@code{memory} provides a single method reporting total
+physical system memory accessible to the kernel. It does not account for memory
+used by other processes.")
+      (license license:bsd-3))))
+
+(define-public go-github-com-surgebase-porter2
+  (let ((commit "56e4718818e8dc4ea5ba6348402fc7661863732a")
+        (revision "1"))
+    (package
+      (name "go-github-com-surgebase-porter2")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/surgebase/porter2")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-surgebase-porter2-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "1ivcf83jlj9s7q5y9dfbpyl0br35cz8fcp0dm8sxxvqh54py06v2"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/surgebase/porter2"))
+      (native-inputs
+       `(("go-github-com-stretchr-testify" ,go-github-com-stretchr-testify)
+         ("go-github-com-surge-glog" ,go-github-com-surge-glog)))
+      (home-page "https://github.com/surgebase/porter2")
+      (synopsis "Go library implementing english Porter2 stemmer")
+      (description "Porter2 implements the
+@url{http://snowball.tartarus.org/algorithms/english/stemmer.html, english
+Porter2 stemmer}.  It is written completely using finite state machines to do
+suffix comparison, rather than the string-based or tree-based approaches.")
+      (license license:asl2.0))))
+
+(define-public go-github-com-surge-glog
+  (let ((commit "2578deb2b95c665e6b1ebabf304ce2085c9e1985")
+        (revision "1"))
+    (package
+      (name "go-github-com-surge-glog")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/surge/glog")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-surge-glog-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "1bxcwxvsvr2hfpjz9hrrn0wrgykwmrbyk567102k3vafw9xdcwk4"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/surge/glog"))
+      (home-page "https://github.com/surge/glog")
+      (synopsis "Leveled execution logs for Go")
+      (description "Leveled execution logs for Go.")
+      (license license:asl2.0))))
-- 
cgit v1.2.3


From 132d494f4e599425c6254279e1452804bbdd5ec9 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 12 Mar 2020 05:46:42 -0500
Subject: gn: remove upstreamed package

---
 gn/packages/python.scm | 3 ---
 1 file changed, 3 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 8493698..88f0156 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1202,9 +1202,6 @@ CLI scripts:
        `(("python2-futures" ,python2-futures)
          ,@(package-propagated-inputs ipyparallel))))))
 
-(define-public python2-pyfaidx
-  (package-with-python2 python-pyfaidx))
-
 (define-public python-admiral
   (package
     (name "python-admiral")
-- 
cgit v1.2.3


From 248c2e3905d75d69e227fe9b474bbd6e0c422789 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 12 Mar 2020 09:45:51 -0500
Subject: gn: edirect-gn: Fix edirect-gn

This commit does many things:
Adjust for upstream update.
Fix the error not allowing us to download new data.
Use self-compiled binaries instead of downloading from upstream.
Install more scripts.
Wrap all the programs and scripts so they can work in a pureenvironment.
---
 gn/packages/bioinformatics.scm | 80 +++++++++++++-----------------------------
 1 file changed, 24 insertions(+), 56 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 6a38499..45e88c7 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -428,45 +428,33 @@ reads.")
       (substitute-keyword-arguments (package-arguments edirect)
         ((#:phases phases)
          `(modify-phases ,phases
-         ;   (replace 'build
-         ;     (lambda* (#:key inputs #:allow-other-keys)
-         ;       (let ((go (string-append (assoc-ref inputs "go") "/bin/go")))
-         ;         (invoke go "build" "xtract.go"))))
-            (add-after 'unpack 'unpack-binaries
-              (lambda* (#:key inputs #:allow-other-keys)
-                (let ((gzip (assoc-ref inputs "gzip"))
-                      (xtract (assoc-ref inputs "xtract.Linux"))
-                      (rchive (assoc-ref inputs "rchive.Linux")))
-                  (copy-file xtract "xtract.Linux.gz")
-                  (copy-file rchive "rchive.Linux.gz")
-                  (invoke (string-append gzip "/bin/gzip") "xtract.Linux.gz" "-dfv")
-                  (invoke (string-append gzip "/bin/gzip") "rchive.Linux.gz" "-dfv"))))
             (add-after 'unpack 'patch-programs
-              (lambda _
-                (substitute* (find-files "." "^e")
-                  (("exec perl") "exec"))
-                (substitute* '("xtract" "rchive")
-                  ;; or add current directory to PATH
-                  ((".*PATH.*") ""))
+              (lambda* (#:key inputs #:allow-other-keys)
+                ;; Ignore errors about missing xtract.Linux and rchive.Linux.
+                (substitute* "pm-refresh"
+                  (("cat \\\"\\$target")
+                   "grep ^[[:digit:]] \"$target"))
                 #t))
             (replace 'install
-              (lambda* (#:key outputs #:allow-other-keys)
-                (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+              (lambda* (#:key inputs outputs #:allow-other-keys)
+                (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+                      (edirect-go (assoc-ref inputs "edirect-go-programs")))
                   (for-each
                     (lambda (file)
                       (install-file file bin))
-                    '("archive-pubmed" "asp-cp" "asp-ls" "download-pubmed"
-                      "edirect.pl" "efetch" "epost" "esearch" "fetch-pubmed"
-                      "ftp-cp" "ftp-ls" "has-asp" "pm-prepare" "pm-refresh"
-                      "pm-stash" "rchive" "xtract"))
-                  (install-file "xtract.Linux" bin)
-                  (install-file "rchive.Linux" bin)
-                  (chmod (string-append bin "/xtract.Linux") #o555)
-                  (chmod (string-append bin "/rchive.Linux") #o555))
+                    '("archive-pubmed" "asp-cp" "asp-ls" "download-ncbi-data"
+                      "download-pubmed" "edirect.pl" "efetch" "epost" "esearch"
+                      "fetch-pubmed" "ftp-cp" "ftp-ls" "has-asp" "index-pubmed"
+                      "pm-prepare" "pm-refresh" "pm-stash" "pm-collect"
+                      "pm-index" "pm-invert" "pm-merge" "pm-promote"))
+                  (symlink (string-append edirect-go "/bin/xtract.Linux")
+                           (string-append bin "/xtract"))
+                  (symlink (string-append edirect-go "/bin/rchive.Linux")
+                           (string-append bin "/rchive")))
                 #t))
             (replace 'wrap-program
               (lambda* (#:key outputs #:allow-other-keys)
-                ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
+                ;; Make sure everything can run in a pure environment.
                 (let ((out (assoc-ref outputs "out"))
                       (path (getenv "PERL5LIB")))
                   (for-each
@@ -474,44 +462,24 @@ reads.")
                       (wrap-program file
                                     `("PERL5LIB" ":" prefix (,path)))
                       (wrap-program file
-                                    `("PATH" ":" prefix (,(dirname (which "sed"))
+                                    `("PATH" ":" prefix (,(string-append out "/bin")
+                                                         ,(dirname (which "sed"))
                                                          ,(dirname (which "gzip"))
+                                                         ,(dirname (which "grep"))
+                                                         ,(dirname (which "perl"))
                                                          ,(dirname (which "uname"))))))
                     (find-files out ".")))
                 #t))))))
     (inputs
-     `(("gzip" ,gzip)
+     `(("edirect-go-programs" ,edirect-go-programs)
        ,@(package-inputs edirect)))
-    (native-inputs
-     `(
-       ;("go" ,go)
-       ("xtract.Linux"
-        ,(origin
-           (method url-fetch)
-           (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect"
-                               "/versions/" (package-version edirect)
-                               "/xtract.Linux.gz"))
-           (sha256
-            (base32
-             "1idzynn446qqjx2wv4jjgsx6cp349d4jy8g9z4gsg9l6sn5dhx53"))))
-       ("rchive.Linux"
-        ,(origin
-           (method url-fetch)
-           (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
-                               "/versions/" (package-version edirect)
-                               "/rchive.Linux.gz"))
-           (sha256
-            (base32
-             "1p65hifv5d6nxg01vjwgy2nw49nssd822a8aj8jv412mhzj95ihv"))))))
     (native-search-paths
      ;; Ideally this should be set for LWP somewhere.
      (list (search-path-specification
             (variable "PERL_LWP_SSL_CA_FILE")
             (file-type 'regular)
             (separator #f)
-            (files '("/etc/ssl/certs/ca-certificates.crt")))))
-    ;; Due to the precompiled binaries we download:
-    (supported-systems '("x86_64-linux"))))
+            (files '("/etc/ssl/certs/ca-certificates.crt")))))))
 
 (define-public edirect-go-programs
   (package
-- 
cgit v1.2.3


From da457bd06f88fddcd7bfa510e7aac6358ffd028d Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 12 Mar 2020 09:49:38 -0500
Subject: services: make genenetwork1 python24

---
 gn/services/genenetwork.scm | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

(limited to 'gn')

diff --git a/gn/services/genenetwork.scm b/gn/services/genenetwork.scm
index 516c124..4693152 100644
--- a/gn/services/genenetwork.scm
+++ b/gn/services/genenetwork.scm
@@ -2,13 +2,13 @@
 
 (use-modules (gnu)
              (gn packages genenetwork)
-             (gn packages python)
+             (gn packages python24)
              (gn packages web))
 (use-service-modules web)
 (use-package-modules python)
 
 (define %mod-python-path
-  (file-append mod-python "/lib/python2.7/site-packages"))
+  (file-append mod-python "/lib/python2.4/site-packages"))
 
 (operating-system
   (host-name "genenetwork")
@@ -22,15 +22,15 @@
   ;; No firmware for VMs
   (firmware '())
 
-  (packages (cons* python-2
+  (packages (cons* python-2.4
                    mod-python
-                   python2-qtlreaper
-                   python2-htmlgen-gn
-                   python2-json-GN1
-                   python2-piddle
-                   python2-pyx-GN1
-                   python2-pyxlwriter
-                   python2-svg-GN1
+                   python24-qtlreaper
+                   ;python24-htmlgen-gn
+                   python24-json-GN1
+                   python24-piddle
+                   python24-pyx-GN1
+                   python24-pyxlwriter
+                   python24-svg-GN1
                    %base-packages))
 
   (services (list (service httpd-service-type
-- 
cgit v1.2.3


From 298ad0afa980f959e5a9a840d1f53c3503566707 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 22 Mar 2020 10:02:11 +0200
Subject: gn: Upstream edirect-gn

---
 gn/packages/bioinformatics.scm | 116 +-----------------
 gn/packages/golang.scm         | 268 -----------------------------------------
 2 files changed, 1 insertion(+), 383 deletions(-)
 delete mode 100644 gn/packages/golang.scm

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 45e88c7..78a55fc 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -10,12 +10,10 @@
   #:use-module (guix build-system ant)
   #:use-module (guix build-system cmake)
   #:use-module (guix build-system gnu)
-  #:use-module (guix build-system go)
   #:use-module (guix build-system python)
   #:use-module (guix build-system trivial)
   #:use-module (guix build-system waf)
   #:use-module (gnu packages)
-  #:use-module (gn packages golang)
   #:use-module (gn packages python)
   #:use-module (gnu packages bioconductor)
   #:use-module (gnu packages bioinformatics)
@@ -26,7 +24,6 @@
   #:use-module (gnu packages datastructures)
   #:use-module (gnu packages fontutils)
   #:use-module (gnu packages gcc)
-  #:use-module (gnu packages golang)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages imagemagick)
   #:use-module (gnu packages jemalloc)
@@ -421,118 +418,7 @@ reads.")
     (license license:non-copyleft)))
 
 (define-public edirect-gn
-  (package
-    (inherit edirect)
-    (name "edirect-gn")
-    (arguments
-      (substitute-keyword-arguments (package-arguments edirect)
-        ((#:phases phases)
-         `(modify-phases ,phases
-            (add-after 'unpack 'patch-programs
-              (lambda* (#:key inputs #:allow-other-keys)
-                ;; Ignore errors about missing xtract.Linux and rchive.Linux.
-                (substitute* "pm-refresh"
-                  (("cat \\\"\\$target")
-                   "grep ^[[:digit:]] \"$target"))
-                #t))
-            (replace 'install
-              (lambda* (#:key inputs outputs #:allow-other-keys)
-                (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
-                      (edirect-go (assoc-ref inputs "edirect-go-programs")))
-                  (for-each
-                    (lambda (file)
-                      (install-file file bin))
-                    '("archive-pubmed" "asp-cp" "asp-ls" "download-ncbi-data"
-                      "download-pubmed" "edirect.pl" "efetch" "epost" "esearch"
-                      "fetch-pubmed" "ftp-cp" "ftp-ls" "has-asp" "index-pubmed"
-                      "pm-prepare" "pm-refresh" "pm-stash" "pm-collect"
-                      "pm-index" "pm-invert" "pm-merge" "pm-promote"))
-                  (symlink (string-append edirect-go "/bin/xtract.Linux")
-                           (string-append bin "/xtract"))
-                  (symlink (string-append edirect-go "/bin/rchive.Linux")
-                           (string-append bin "/rchive")))
-                #t))
-            (replace 'wrap-program
-              (lambda* (#:key outputs #:allow-other-keys)
-                ;; Make sure everything can run in a pure environment.
-                (let ((out (assoc-ref outputs "out"))
-                      (path (getenv "PERL5LIB")))
-                  (for-each
-                    (lambda (file)
-                      (wrap-program file
-                                    `("PERL5LIB" ":" prefix (,path)))
-                      (wrap-program file
-                                    `("PATH" ":" prefix (,(string-append out "/bin")
-                                                         ,(dirname (which "sed"))
-                                                         ,(dirname (which "gzip"))
-                                                         ,(dirname (which "grep"))
-                                                         ,(dirname (which "perl"))
-                                                         ,(dirname (which "uname"))))))
-                    (find-files out ".")))
-                #t))))))
-    (inputs
-     `(("edirect-go-programs" ,edirect-go-programs)
-       ,@(package-inputs edirect)))
-    (native-search-paths
-     ;; Ideally this should be set for LWP somewhere.
-     (list (search-path-specification
-            (variable "PERL_LWP_SSL_CA_FILE")
-            (file-type 'regular)
-            (separator #f)
-            (files '("/etc/ssl/certs/ca-certificates.crt")))))))
-
-(define-public edirect-go-programs
-  (package
-    (inherit edirect)
-    (name "edirect-go-programs")
-    (build-system go-build-system)
-    (arguments
-     `(#:install-source? #f
-       #:tests? #f      ; No tests.
-       #:import-path "ncbi.nlm.nih.gov/entrez/edirect"
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'replace-go-dependency
-           ;; This go library does not have any license.
-           ;; TODO: This should move to a source snippet.
-           (lambda* (#:key import-path #:allow-other-keys)
-             (with-directory-excursion (string-append "src/" import-path)
-               (substitute* "rchive.go"
-                 (("github.com/fiam/gounidecode/unidecode")
-                  "golang.org/rainycape/unidecode"))
-               #t)))
-         (replace 'build
-           (lambda* (#:key import-path #:allow-other-keys)
-             (with-directory-excursion (string-append "src/" import-path)
-               (invoke "go" "build" "-v" "-x" "j2x.go")
-               (invoke "go" "build" "-v" "-x" "t2x.go")
-               (invoke "go" "build" "-v" "-x" "-o"
-                       "xtract.Linux" "xtract.go" "common.go")
-               (invoke "go" "build" "-v" "-x" "-o"
-                       "rchive.Linux" "rchive.go" "common.go")
-               (invoke "go" "build" "-v" "-x" "-o" "symbols.Linux" "s2p.go"))))
-         (replace 'install
-           (lambda* (#:key outputs import-path #:allow-other-keys)
-             (let ((dest    (string-append (assoc-ref outputs "out") "/bin"))
-                   (source  (string-append "src/" import-path "/")))
-               (for-each (lambda (file)
-                           (format #t "installing ~a~%" file)
-                           (install-file (string-append source file) dest))
-                         '("j2x" "t2x" "symbols.Linux" "xtract.Linux" "rchive.Linux"))
-               #t))))))
-    (native-inputs '())
-    (propagated-inputs '())
-    (inputs
-     `(("go-github-com-fatih-color" ,go-github-com-fatih-color)
-       ("go-github-com-fogleman-gg" ,go-github-com-fogleman-gg)
-       ("go-github-com-gedex-inflector" ,go-github-com-gedex-inflector)
-       ("go-github-com-golang-freetype" ,go-github-com-golang-freetype)
-       ("go-github-com-klauspost-cpuid" ,go-github-com-klauspost-cpuid)
-       ("go-github-com-pbnjay-memory" ,go-github-com-pbnjay-memory)
-       ("go-github-com-surgebase-porter2" ,go-github-com-surgebase-porter2)
-       ("go-golang-org-rainycape-unidecode" ,go-golang-org-rainycape-unidecode)
-       ("go-golang-org-x-image" ,go-golang-org-x-image)
-       ("go-golang-org-x-text" ,go-golang-org-x-text)))))
+  (deprecated-package "edirect-gn" edirect))
 
 ;; TODO: Unbundle zlib, bamtools, tclap
 (define-public sniffles
diff --git a/gn/packages/golang.scm b/gn/packages/golang.scm
deleted file mode 100644
index 56eed66..0000000
--- a/gn/packages/golang.scm
+++ /dev/null
@@ -1,268 +0,0 @@
-(define-module (gn packages golang)
-  #:use-module ((guix licenses) #:prefix license:)
-  #:use-module (guix git-download)
-  #:use-module (guix packages)
-  #:use-module (guix utils)
-  #:use-module (guix build-system go)
-  #:use-module (gnu packages golang)
-  )
-
-(define-public go-golang-org-x-image
-  (let ((commit "58c23975cae11f062d4b3b0c143fe248faac195d")
-        (revision "1"))
-    (package
-      (name "go-golang-org-x-image")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://go.googlesource.com/image")
-                       (commit commit)))
-                (file-name (string-append "go.googlesource.com-image-"
-                                          version "-checkout"))
-                (sha256
-                 (base32
-                  "0i2p2girc1sfcic6xs6vrq0fp3szfx057xppksb67kliywjjrm5x"))))
-      (build-system go-build-system)
-      (arguments
-       `(#:import-path "golang.org/x/image"
-         ; Source-only package
-         #:tests? #f
-         #:phases
-         (modify-phases %standard-phases
-           (delete 'build))))
-      (home-page "https://go.googlesource.com/image")
-      (synopsis "Supplemental Go image libraries")
-      (description "This package provides supplemental Go libraries for image
-processing.")
-      (license license:bsd-3))))
-
-(define-public go-github-com-fiam-gounidecode
-  (let ((commit "311ebb7422d3ff70cc1d064c5a297520ff5f304a")
-        (revision "1"))
-    (package
-      (name "go-github-com-fiam-gounidecode")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/fiam/gounidecode")
-                       (commit commit)))
-                (file-name (string-append "go-github-com-fiam-gounidecode-"
-                                          version "-checkout"))
-                (sha256
-                 (base32
-                  "107c2qnlgl9d55pww3kh3x5m5pqw7ijzzqbpsrpxnzn5jls44xbs"))))
-      (build-system go-build-system)
-      (arguments
-       `(#:unpack-path "github.com/fiam/gounidecode"
-         #:import-path "github.com/fiam/gounidecode/unidecode"))
-      (home-page "https://github.com/fiam/gounidecode/")
-      (synopsis "Unicode transliterator for Go")
-      (description "Unicode transliterator for Go.")
-      (license #f))))       ; No license listed.
-
-(define-public go-golang-org-rainycape-unidecode
-  (let ((commit "cb7f23ec59bec0d61b19c56cd88cee3d0cc1870c")
-        (revision "1"))
-    (package
-      (name "go-golang-org-rainycape-unidecode")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/rainycape/unidecode")
-                       (commit commit)))
-                (file-name (string-append "go-golang-org-rainycape-unidecode-"
-                                          version "-checkout"))
-                (sha256
-                 (base32
-                  "1wvzdijd640blwkgmw6h09frkfa04kcpdq87n2zh2ymj1dzla5v5"))))
-      (build-system go-build-system)
-      (arguments
-       `(#:import-path "golang.org/rainycape/unidecode"))
-      (home-page "https://github.com/rainycape/unidecode")
-      (synopsis "Unicode transliterator in Golang")
-      (description "Unicode transliterator in Golang - Replaces non-ASCII
-characters with their ASCII approximations.")
-      (license license:asl2.0))))
-
-(define-public go-github-com-golang-freetype
-  (let ((commit "e2365dfdc4a05e4b8299a783240d4a7d5a65d4e4")
-        (revision "1"))
-    (package
-      (name "go-github-com-golang-freetype")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/golang/freetype")
-                       (commit commit)))
-                (file-name (string-append "go-github-com-golang-freetype-"
-                                          version "-checkout"))
-                (sha256
-                 (base32
-                  "194w3djc6fv1rgcjqds085b9fq074panc5vw582bcb8dbfzsrqxc"))))
-      (build-system go-build-system)
-      (arguments
-       `(#:import-path "github.com/golang/freetype"))
-      (propagated-inputs
-       `(("go-golang-org-x-image" ,go-golang-org-x-image)))
-      (home-page "https://github.com/golang/freetype")
-      (synopsis "Freetype font rasterizer in the Go programming language")
-      (description "The Freetype font rasterizer in the Go programming language.")
-      (license (list license:freetype
-                     license:gpl2+)))))
-
-(define-public go-github-com-fogleman-gg
-  (package
-    (name "go-github-com-fogleman-gg")
-    (version "1.3.0")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/fogleman/gg")
-                     (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1nkldjghbqnzj2djfaxhiv35kk341xhcrj9m2dwq65v684iqkk8n"))))
-    (build-system go-build-system)
-    (arguments
-     `(#:tests? #f      ; Issue with test flags.
-       #:import-path "github.com/fogleman/gg"))
-    (propagated-inputs
-     `(("go-github-com-golang-freetype" ,go-github-com-golang-freetype)))
-    (home-page "https://github.com/fogleman/gg")
-    (synopsis "2D rendering in Go")
-    (description "@code{gg} is a library for rendering 2D graphics in pure Go.")
-    (license license:expat)))
-
-(define-public go-github-com-gedex-inflector
-  (let ((commit "16278e9db8130ac7ec405dc174cfb94344f16325")
-        (revision "1"))
-    (package
-      (name "go-github-com-gedex-inflector")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/gedex/inflector")
-                       (commit commit)))
-                (file-name (string-append "go-github-com-gedex-inflector-"
-                                          version "-checkout"))
-                (sha256
-                 (base32
-                  "05hjqw1m71vww4914d9h6nqa9jw3lgjzwsy7qaffl02s2lh1amks"))))
-      (build-system go-build-system)
-      (arguments
-       `(#:import-path "github.com/gedex/inflector"))
-      (home-page "https://github.com/gedex/inflector")
-      (synopsis "Go library that pluralizes and singularizes English nouns")
-      (description "Go library that pluralizes and singularizes English nouns.")
-      (license license:bsd-2))))
-
-(define-public go-github-com-klauspost-cpuid
-  (package
-    (name "go-github-com-klauspost-cpuid")
-    (version "1.2.3")
-    (source (origin
-              (method git-fetch)
-              (uri (git-reference
-                     (url "https://github.com/klauspost/cpuid")
-                     (commit (string-append "v" version))))
-              (file-name (git-file-name name version))
-              (sha256
-               (base32
-                "1s510210wdj5dkamii1qrk7v87k4qpdcrrjzflp5ha9iscw6b06l"))))
-    (build-system go-build-system)
-    (arguments
-     `(#:import-path "github.com/klauspost/cpuid"))
-    (home-page "https://github.com/klauspost/cpuid")
-    (synopsis "CPU feature identification for Go")
-    (description "@code{cpuid} provides information about the CPU running the
-current program.  CPU features are detected on startup, and kept for fast access
-through the life of the application. Currently x86 / x64 (AMD64) is supported,
-and no external C (cgo) code is used, which should make the library very eas
-to use.")
-    (license license:expat)))
-
-(define-public go-github-com-pbnjay-memory
-  (let ((commit "974d429e7ae40c89e7dcd41cfcc22a0bfbe42510")
-        (revision "1"))
-    (package
-      (name "go-github-com-pbnjay-memory")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/pbnjay/memory")
-                       (commit commit)))
-                (file-name (string-append "go-github-com-pbnjay-memory-"
-                                          version "-checkout"))
-                (sha256
-                 (base32
-                  "0kazg5psdn90pqadrzma5chdwh0l2by9z31sspr47gx93fhjmkkq"))))
-      (build-system go-build-system)
-      (arguments
-       `(#:import-path "github.com/pbnjay/memory"))
-      (home-page "https://github.com/gedex/inflector")
-      (synopsis "Go library to report total system memory")
-      (description "@code{memory} provides a single method reporting total
-physical system memory accessible to the kernel. It does not account for memory
-used by other processes.")
-      (license license:bsd-3))))
-
-(define-public go-github-com-surgebase-porter2
-  (let ((commit "56e4718818e8dc4ea5ba6348402fc7661863732a")
-        (revision "1"))
-    (package
-      (name "go-github-com-surgebase-porter2")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/surgebase/porter2")
-                       (commit commit)))
-                (file-name (string-append "go-github-com-surgebase-porter2-"
-                                          version "-checkout"))
-                (sha256
-                 (base32
-                  "1ivcf83jlj9s7q5y9dfbpyl0br35cz8fcp0dm8sxxvqh54py06v2"))))
-      (build-system go-build-system)
-      (arguments
-       `(#:import-path "github.com/surgebase/porter2"))
-      (native-inputs
-       `(("go-github-com-stretchr-testify" ,go-github-com-stretchr-testify)
-         ("go-github-com-surge-glog" ,go-github-com-surge-glog)))
-      (home-page "https://github.com/surgebase/porter2")
-      (synopsis "Go library implementing english Porter2 stemmer")
-      (description "Porter2 implements the
-@url{http://snowball.tartarus.org/algorithms/english/stemmer.html, english
-Porter2 stemmer}.  It is written completely using finite state machines to do
-suffix comparison, rather than the string-based or tree-based approaches.")
-      (license license:asl2.0))))
-
-(define-public go-github-com-surge-glog
-  (let ((commit "2578deb2b95c665e6b1ebabf304ce2085c9e1985")
-        (revision "1"))
-    (package
-      (name "go-github-com-surge-glog")
-      (version (git-version "0.0.0" revision commit))
-      (source (origin
-                (method git-fetch)
-                (uri (git-reference
-                       (url "https://github.com/surge/glog")
-                       (commit commit)))
-                (file-name (string-append "go-github-com-surge-glog-"
-                                          version "-checkout"))
-                (sha256
-                 (base32
-                  "1bxcwxvsvr2hfpjz9hrrn0wrgykwmrbyk567102k3vafw9xdcwk4"))))
-      (build-system go-build-system)
-      (arguments
-       `(#:import-path "github.com/surge/glog"))
-      (home-page "https://github.com/surge/glog")
-      (synopsis "Leveled execution logs for Go")
-      (description "Leveled execution logs for Go.")
-      (license license:asl2.0))))
-- 
cgit v1.2.3


From c0e65765322c9d6a8de7c60e51edce098826adac Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 15 Mar 2020 08:24:48 -0500
Subject: gn: Add r-tictoc.

---
 gn/packages/cran.scm | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 gn/packages/cran.scm

(limited to 'gn')

diff --git a/gn/packages/cran.scm b/gn/packages/cran.scm
new file mode 100644
index 0000000..ed4d925
--- /dev/null
+++ b/gn/packages/cran.scm
@@ -0,0 +1,29 @@
+(define-module (gnu packages cran)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system r)
+  #:use-module (gnu packages))
+
+(define-public r-tictoc
+  (package
+    (name "r-tictoc")
+    (version "1.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "tictoc" version))
+        (sha256
+         (base32
+          "1zp2n8k2ax2jjw89dsri268asmm5ry3ijf32wbca5ji231y0knj7"))))
+    (build-system r-build-system)
+    (home-page "http://github.com/collectivemedia/tictoc")
+    (synopsis "Functions for timing R scripts")
+    (description
+     "This package provides the timing functions @code{tic} and @code{toc} that
+can be nested.  One can record all timings while a complex script is running,
+and examine the values later.  It is also possible to instrument the timing call
+with custom callbacks.  In addition, this package provides class 'Stack',
+implemented as a vector, and class 'List', implemented as a list, both of whic
+support operations 'push', 'pop', 'first', 'last' and 'clear'.")
+    (license license:asl2.0)))
-- 
cgit v1.2.3


From febe9d081cd6c09cef86693e680143e93bfd67ea Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 22 Mar 2020 07:08:27 -0500
Subject: gn: Adjust for upstream changes

---
 gn/packages/jupyterhub.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gn')

diff --git a/gn/packages/jupyterhub.scm b/gn/packages/jupyterhub.scm
index 5b69b5b..43da8ec 100644
--- a/gn/packages/jupyterhub.scm
+++ b/gn/packages/jupyterhub.scm
@@ -15,6 +15,7 @@
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages rpc)
   #:use-module (gnu packages serialization)
   #:use-module (gnu packages time)
   #:use-module (gn packages node))
-- 
cgit v1.2.3


From 7f4226ea033a1b4207609741eed95d97f03f3158 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 22 Mar 2020 07:11:56 -0500
Subject: fix typo

---
 gn/packages/cran.scm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'gn')

diff --git a/gn/packages/cran.scm b/gn/packages/cran.scm
index ed4d925..d92f9f3 100644
--- a/gn/packages/cran.scm
+++ b/gn/packages/cran.scm
@@ -1,4 +1,4 @@
-(define-module (gnu packages cran)
+(define-module (gn packages cran)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix packages)
   #:use-module (guix download)
-- 
cgit v1.2.3


From b5177650f425afb5fdc9147904d7cb0e7437e0cb Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 31 Mar 2020 08:35:21 -0500
Subject: gn: ratspub: Adjust to edirect-gn upstreaming.

---
 gn/packages/ratspub.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 290b9e2..694379a 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -4,7 +4,7 @@
   #:use-module (guix git-download)
   #:use-module (guix build-system python)
   #:use-module (gnu packages admin)
-  #:use-module (gn packages bioinformatics)
+  #:use-module (gnu packages bioinformatics)
   #:use-module (gn packages javascript)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
@@ -72,7 +72,7 @@
                  `("PYTHONPATH" ":" prefix (,path))))
              #t)))))
     (inputs
-     `(("edirect" ,edirect-gn)
+     `(("edirect" ,edirect)
        ("inetutils" ,inetutils)
        ("python-flask" ,python-flask)
        ("python-nltk" ,python-nltk)))
@@ -89,4 +89,4 @@ the question \"What do we know about these genes and addiction?\".  Data from
 @acronym{EBI GWAS, European Bioinformatics Institute Genome-Wide Association
 Studies} catalog are also included in the search to better answer this
 question.")
-    (license #f)))
+    (license license:expat)))
-- 
cgit v1.2.3


From 14dc7e6f85f204d01fc5a96e986469c0355e87fb Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 15 Mar 2020 04:33:59 -0500
Subject: gn: ratspub: Update to 0.2.2.

---
 gn/packages/javascript.scm | 24 ++++++++++++++
 gn/packages/ratspub.scm    | 80 ++++++++++++++++++++++++++++++++++------------
 2 files changed, 83 insertions(+), 21 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm
index 79a8060..95d4154 100644
--- a/gn/packages/javascript.scm
+++ b/gn/packages/javascript.scm
@@ -1121,3 +1121,27 @@ widgets, and themes built on top of the jQuery JavaScript Library.")
     (name "js-jquery-ui")
     (arguments `(#:javascript-files '("ui/jquery-ui.js")))
     (build-system minify-build-system)))
+
+(define-public js-popper
+  (package
+    (name "js-popper")
+    (version "2.0.6")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+              (url "https://github.com/popperjs/popper-core")
+              (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "0lzy981p9nja2l3xa2zvals6q31v3bzpxxa85yn9pm7wkj3vglf2"))))
+    (build-system minify-build-system)
+    (arguments
+     `(#:javascript-files '("src/popper.js")))
+    (home-page "https://popper.js.org/")
+    (synopsis "Tooltip and popover positioning engine")
+    (description
+     "Given an element, such as a button, and a tooltip element describing it,
+Popper will automatically put the tooltip in the right place near the button.")
+    (license license:expat)))
diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 694379a..3e5727c 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -6,6 +6,8 @@
   #:use-module (gnu packages admin)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gn packages javascript)
+  #:use-module (gnu packages time)
+  #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
   #:use-module (gn packages web))
@@ -13,16 +15,16 @@
 (define-public ratspub
   (package
     (name "ratspub")
-    (version "0.1")
+    (version "0.2.2")
     (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://github.com/chen42/ratspub.git")
-                   (commit (string-append "v" version))))
-             (file-name (git-file-name name version))
-             (sha256
-              (base32
-               "0cm9g38fxpa52458mdmhzhghj5c7b8l3k1b764zs9hdrki5s7wi7"))))
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/chen42/ratspub.git")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "0q111fsch69kjv96d0pld9agqpwazh9p47vsvig63hmmjp72wa84"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f ; no test suite
@@ -34,12 +36,24 @@
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out       (assoc-ref outputs "out"))
                    (inetutils (assoc-ref inputs "inetutils")))
-               (substitute* "templates/cytoscape.html"
+               (substitute* '("templates/cytoscape.html"
+                              "templates/tableview.html"
+                              "templates/tableview0.html"
+                              "templates/userarchive.html")
                  (("script src=.*")
                   "script src=\"/static/cytoscape.min.js\"></script>\n"))
                (substitute* "templates/layout.html"
-                 (("https://stackpath.bootstrapcdn.com/bootstrap/.*")
-                  "/static/bootstrap.min.css\">\n"))
+                 (("https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css.*")
+                  "/static/bootstrap.min.css\">\n")
+                 (("https://.*.bootstrapcdn.com/bootstrap/4.*/js/bootstrap.min.js.*")
+                  "/static/bootstrap.min.js\"></script>\n")
+                 (("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css")
+                  "/static/font-awesome.min.css")
+                 (("https://code.jquery.com/jquery-3.2.1.slim.min.js.*")
+                  "/static/jquery.slim.min.js\"></script>\n")
+                 ;(("https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js.*")
+                 ; "/static/popper.min.js\"></script>\n")
+                 )
                (substitute* "ratspub.py"
                  (("hostname") (string-append inetutils "/bin/hostname"))))
              #t))
@@ -51,34 +65,58 @@
          (add-after 'install 'install-javascript
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out       (assoc-ref outputs "out"))
+                   (awesome   (assoc-ref inputs "font-awesome"))
+                   (bootstrap (assoc-ref inputs "bootstrap"))
                    (cytoscape (assoc-ref inputs "cytoscape"))
-                   (bootstrap (assoc-ref inputs "bootstrap")))
+                   (jquery    (assoc-ref inputs "jquery"))
+                   ;(js-popper (assoc-ref inputs "js-popper"))
+                   )
+               (symlink (string-append awesome
+                                       "/share/web/font-awesomecss/font-awesome.min.css")
+                        (string-append out "/static/font-awesome.min.css"))
+               (symlink (string-append bootstrap
+                                       "/share/web/bootstrap/css/bootstrap.min.css")
+                        (string-append out "/static/bootstrap.min.css"))
+               (symlink (string-append bootstrap
+                                       "/share/web/bootstrap/js/bootstrap.min.js")
+                        (string-append out "/static/bootstrap.min.js"))
                (symlink (string-append cytoscape
                                        "/share/genenetwork2/javascript/cytoscape/cytoscape.min.js")
                         (string-append out "/static/cytoscape.min.js"))
-               (symlink (string-append bootstrap
-                                       "/share/web/bootstrap/css/bootstrap.min.css")
-                        (string-append out "/static/bootstrap.min.css")))
+               (symlink (string-append jquery
+                                       "/share/web/jquery/jquery.slim.min.js")
+                        (string-append out "/static/jquery.slim.min.js"))
+               ;(symlink (string-append js-popper
+               ;                        "/share/web/popper/popper.min.js")
+               ;         (string-append out "/static/popper.min.js"))
+               )
              #t))
          (add-after 'install 'wrap-executable
            (lambda* (#:key inputs outputs #:allow-other-keys)
              (let ((out  (assoc-ref outputs "out"))
                    (path (getenv "PYTHONPATH")))
                (wrap-program (string-append out "/server.py")
-                 `("PATH" ":" prefix (,(dirname (which "edirect.pl"))
+                `("PATH" ":" prefix (,(dirname (which "edirect.pl"))
                                       ,(dirname (which "dirname"))
                                       ,(dirname (which "grep"))
                                       ,(dirname (which "sed"))))
-                 `("PYTHONPATH" ":" prefix (,path))))
+                `("PYTHONPATH" ":" prefix (,path))))
              #t)))))
     (inputs
      `(("edirect" ,edirect)
        ("inetutils" ,inetutils)
+       ("python-bcrypt" ,python-bcrypt)
        ("python-flask" ,python-flask)
-       ("python-nltk" ,python-nltk)))
+       ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+       ("python-nltk" ,python-nltk)
+       ("python-pytz" ,python-pytz)))
     (native-inputs
-     `(("cytoscape" ,javascript-cytoscape)
-       ("bootstrap" ,web-bootstrap)))
+     `(("bootstrap" ,web-bootstrap)
+       ("cytoscape" ,javascript-cytoscape)
+       ("font-awesome" ,web-font-awesome)
+       ("jquery" ,web-jquery)
+       ;("js-popper" ,js-popper)
+       ))
     (home-page "http://rats.pub/")
     (synopsis "Relationship with Addiction Through Searches of PubMed")
     (description
-- 
cgit v1.2.3


From ba6cc50345c46463cb3dda0842cd85015a2b20e9 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 7 Apr 2020 21:09:24 +0300
Subject: gn: Upstream 2 python packages

---
 gn/packages/python.scm | 106 -------------------------------------------------
 1 file changed, 106 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 88f0156..17cd7ae 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1096,112 +1096,6 @@ spreadsheets without the need for COM objects.")
     (description "")
     (license license:bsd-4)))
 
-(define-public python-ipython-cluster-helper
-  (package
-    (name "python-ipython-cluster-helper")
-    (version "0.6.4")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "ipython-cluster-helper" version))
-        (sha256
-         (base32
-          "1l6mlwxlkxpbvawfwk6qffich7ahg9hq2bxfissgz6144p3k4arj"))
-        (modules '((guix build utils)))
-        (snippet
-         '(begin (substitute* "requirements.txt"
-                   (("ipython.*") "ipython\n"))
-                 #t))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f      ; Test suite can't find IPython.
-       #:phases
-       (modify-phases %standard-phases
-         (replace 'check
-           (lambda* (#:key inputs outputs tests? #:allow-other-keys)
-             (if tests?
-               (begin
-                 (setenv "HOME" (getcwd))
-                 (add-installed-pythonpath inputs outputs)
-                 (invoke "python" "example/example.py" "--local"))
-               #t))))))
-    (propagated-inputs
-     `(("python-ipyparallel" ,python-ipyparallel)
-       ("python-ipython" ,python-ipython)
-       ("python-netifaces" ,python-netifaces)
-       ("python-pyzmq" ,python-pyzmq)
-       ("python-setuptools" ,python-setuptools)
-       ("python-six" ,python-six)))
-    (home-page "https://github.com/roryk/ipython-cluster-helper")
-    (synopsis
-     "Simplify IPython cluster start up and use for multiple schedulers")
-    (description
-     "@code{ipython-cluster-helper} creates a throwaway parallel IPython
-profile, launches a cluster and returns a view.  On program exit it shuts the
-cluster down and deletes the throwaway profile.")
-    (license license:expat)))
-
-(define-public python2-ipython-cluster-helper
-  (package-with-python2 python-ipython-cluster-helper))
-
-(define-public python-ipyparallel
-  (package
-    (name "python-ipyparallel")
-    (version "6.2.4")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "ipyparallel" version))
-        (sha256
-         (base32
-          "0rf0dbpxf5z82bw8lsjj45r3wdd4wc74anz4wiiaf2rbjqlb1ivn"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f ; RuntimeError: IO Loop failed to start
-       #:phases
-       (modify-phases %standard-phases
-         (add-before 'check 'prepare-for-tests
-           (lambda _
-             (setenv "HOME" (getcwd))
-             #t)))))
-    (propagated-inputs
-     `(("python-dateutil" ,python-dateutil)
-       ("python-decorator" ,python-decorator)
-       ("python-ipykernel" ,python-ipykernel)
-       ("python-ipython" ,python-ipython)
-       ("python-ipython-genutils" ,python-ipython-genutils)
-       ("python-jupyter-client" ,python-jupyter-client)
-       ("python-pyzmq" ,python-pyzmq)
-       ("python-tornado" ,python-tornado)
-       ("python-traitlets" ,python-traitlets)))
-    (native-inputs
-     `(("python-ipython" ,python-ipython)
-       ("python-mock" ,python-mock)
-       ("python-nose" ,python-nose)
-       ("python-pytest" ,python-pytest)
-       ("python-pytest-cov" ,python-pytest-cov)
-       ("python-testpath" ,python-testpath)))
-    (home-page "https://ipython.org/")
-    (synopsis "Interactive Parallel Computing with IPython")
-    (description
-     "@code{ipyparallel} is a Python package and collection of CLI scripts for
-controlling clusters for Jupyter.  @code{ipyparallel} contains the following
-CLI scripts:
-@enumerate
-@item ipcluster - start/stop a cluster
-@item ipcontroller - start a scheduler
-@item ipengine - start an engine
-@end enumerate")
-    (license license:bsd-3)))
-
-(define-public python2-ipyparallel
-  (let ((ipyparallel (package-with-python2 python-ipyparallel)))
-    (package
-      (inherit ipyparallel)
-      (propagated-inputs
-       `(("python2-futures" ,python2-futures)
-         ,@(package-propagated-inputs ipyparallel))))))
-
 (define-public python-admiral
   (package
     (name "python-admiral")
-- 
cgit v1.2.3


From c91739a73f438a1fbf63669b93fd8e7a4bf83b32 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Fri, 10 Apr 2020 07:00:06 -0500
Subject: gn: Add diagnostic-slider

---
 gn/packages/bioinformatics.scm | 51 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 51 insertions(+)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 78a55fc..3e276af 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1175,3 +1175,54 @@ variants, performing sequence assembly at the breakpoints, and reconstructing
 the complex structural variants using the long-fragment information from the
 10x Genomics platform.")
       (license license:expat))))
+
+(define-public diagnostic-slider
+  (let ((commit "514d65d4982133e4869e578c5553fced4c6d506c")
+        (revision "1"))
+    (package
+      (name "diagnostic-slider")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/sens/diagnostic-slider")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "04g8if32g8syg6v0bd3jjn05i3d394nx8i3ccl0883p8mlmdvlmx"))))
+      (build-system trivial-build-system)
+      (arguments
+       `(#:modules ((guix build utils))
+         #:builder
+         (begin
+           (use-modules (guix build utils))
+           (let* ((out       (assoc-ref %outputs "out"))
+                  (targetdir (string-append out "/share/" ,name))
+                  (app       (string-append out "/bin/" ,name))
+                  (Rbin      (string-append (assoc-ref %build-inputs "r-min")
+                                            "/bin/Rscript"))
+                  (source    (assoc-ref %build-inputs "source")))
+             (copy-recursively source targetdir)
+             (mkdir-p (string-append out "/bin"))
+             (call-with-output-file app
+               (lambda (port)
+                 (format port
+"#!~a
+library(shiny)
+setwd(\"~a\")
+runApp(launch.browser=0, port=4206)~%\n"
+                         Rbin targetdir)))
+               (chmod app #o555)
+               #t))))
+        (native-inputs
+         `(("source" ,source)))
+        (inputs
+         `(("r-min" ,r-minimal)))
+        (propagated-inputs
+         `(("r" ,r)
+           ("r-shiny" ,r-shiny)))
+        (home-page "https://github.com/sens/diagnostic-slider")
+        (synopsis "")
+        (description
+         "")
+        (license #f))))
-- 
cgit v1.2.3


From 68ba926a0217ac08de4b820c9e2068de6709bd3c Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Fri, 10 Apr 2020 08:46:21 -0500
Subject: gn: Add bh20-seq-resource.

---
 gn/packages/bioinformatics.scm | 132 ++++++++++++++++++++++++++++++++++++++++-
 1 file changed, 131 insertions(+), 1 deletion(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 3e276af..09a706b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -34,9 +34,13 @@
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
   #:use-module (gnu packages python-science)
+  #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages rdf)
   #:use-module (gnu packages readline)
-  #:use-module (gnu packages statistics))
+  #:use-module (gnu packages serialization)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages time))
 
 (define-public contra
   (package
@@ -1226,3 +1230,129 @@ runApp(launch.browser=0, port=4206)~%\n"
         (description
          "")
         (license #f))))
+
+(define-public bh20-seq-resource
+  (let ((commit "ddabd9390d2b221786ef58a6d85200eecf82ca2f")
+        (revision "1"))
+    (package
+      (name "bh20-seq-resource")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/arvados/bh20-seq-resource")
+                       (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32 "04j8b7rz1vqczm6dlyvf1gx58idjhy0swmjbz4bm5r4zgpkps6mb"))))
+      (build-system python-build-system)
+      (inputs
+       `(("python-arvados-python-client" ,python-arvados-python-client)
+         ("python-flask" ,python-flask)
+         ("python-pyyaml" ,python-pyyaml)
+         ("python-schema-salad" ,python-schema-salad)))
+      (native-inputs
+       `(("git" ,(@ (gnu packages version-control) git))
+         ("python-oauth2client" ,python-oauth2client)
+         ("python-pytest" ,python-pytest)
+         ("python-pytest-runner" ,python-pytest-runner)
+         ("python-uritemplate" ,python-uritemplate)))
+      (home-page "https://github.com/arvados/bh20-seq-resource")
+      (synopsis
+       "Tool to upload SARS-CoV-19 sequences and service to kick off analysis")
+      (description "This repository provides a sequence uploader for the
+COVID-19 Virtual Biohackathon's Public Sequence Resource project.  You can use
+it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely
+available to other researchers.")
+      (license license:asl2.0))))
+
+(define-public python-arvados-python-client
+  (package
+    (name "python-arvados-python-client")
+    (version "2.0.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "arvados-python-client" version))
+        (sha256
+         (base32
+          "1a363kdykj5jcrvh3q8wz06g6pqfnm2z48nfy64bls25pkiac1lr"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f  ; tests not included?
+       #:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'loosen-version-requirements
+           (lambda _
+             (substitute* "setup.py"
+               (("ruamel.yaml.*") "ruamel.yaml',\n")
+               (("pbr<1.7.0") "pbr"))
+             #t)))))
+    (propagated-inputs
+     `(("python-ciso8601" ,python-ciso8601)
+       ("python-future" ,python-future)
+       ;("python-google-api-python-client" ,python-google-api-python-client)
+       ("python-google-api-client" ,python-google-api-client)
+       ("python-httplib2" ,python-httplib2)
+       ("python-pycurl" ,python-pycurl)
+       ("python-ruamel.yaml" ,python-ruamel.yaml)
+       ("python-setuptools" ,python-setuptools)
+       ("python-ws4py" ,python-ws4py)))
+    (native-inputs
+     `(("python-mock" ,python-mock)
+       ("python-oauth2client" ,python-oauth2client)
+       ("python-pbr" ,python-pbr)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-uritemplate" ,python-uritemplate)))
+    (home-page "https://arvados.org")
+    (synopsis "Arvados client library")
+    (description "This package provides the arvados module, an API client for
+Arvados.  It also includes higher-level functions to help you write Crunch
+scripts, and command-line tools to store and retrieve data in the Keep storage
+server.")
+    (license license:asl2.0)))
+
+(define-public python-schema-salad
+  (package
+    (name "python-schema-salad")
+    (version "5.0.20200302192450")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "schema-salad" version))
+        (sha256
+         (base32
+          "14vqmfnnvpdaqpajwzi9gyjxx4y2mbgi3y5x3kwk2zqjnnadciv3"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'loosen-version-requirements
+           (lambda _
+             (substitute* "setup.py"
+               (("CacheControl.*") "CacheControl',\n"))
+             #t)))))
+    (propagated-inputs
+     `(("python-cachecontrol" ,python-cachecontrol)
+       ("python-lockfile" ,python-lockfile)
+       ("python-mistune" ,python-mistune)
+       ("python-rdflib" ,python-rdflib)
+       ("python-rdflib-jsonld" ,python-rdflib-jsonld)
+       ("python-requests" ,python-requests)
+       ("python-ruamel.yaml" ,python-ruamel.yaml)
+       ("python-setuptools" ,python-setuptools)
+       ("python-typing-extensions" ,python-typing-extensions)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-runner" ,python-pytest-runner)))
+    (home-page "https://github.com/common-workflow-language/schema_salad")
+    (synopsis "Schema Annotations for Linked Avro Data (SALAD)")
+    (description
+     "Salad is a schema language for describing JSON or YAML structured linked
+data documents.  Salad schema describes rules for preprocessing, structural
+validation, and hyperlink checking for documents described by a Salad schema.
+Salad supports rich data modeling with inheritance, template specialization,
+object identifiers, object references, documentation generation, code
+generation, and transformation to RDF.  Salad provides a bridge between document
+and record oriented data modeling and the Semantic Web.")
+    (license license:asl2.0)))
-- 
cgit v1.2.3


From 6958c2828dfd2247c23d4380f6a0646e51441040 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 12 Apr 2020 09:46:07 +0300
Subject: gn: remove upstreamed package

---
 gn/packages/python.scm | 19 -------------------
 1 file changed, 19 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 17cd7ae..e285880 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -229,25 +229,6 @@ until a value is returned.")
     "A library for W3C Provenance Data Model supporting PROV-JSON, PROV-XML and PROV-O (RDF)")
   (license license:expat)))
 
-(define-public python-typing-extensions; guix candidate
-  (package
-    (name "python-typing-extensions")
-    (version "3.6.6")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "typing_extensions" version))
-        (sha256
-         (base32
-          "07vhddjnd3mhdijyc3s0mwi9jgfjp3rr056nxqiavydbvkrvgrsi"))))
-    (build-system python-build-system)
-    (home-page "https://pypi.python.org/pypi/typing_extensions")
-    (synopsis "Python typing_extensions.")
-    (description
-     "Python typing_extensions.")
-    (license license:gpl2))
-)
-
 (define-public python-subprocess32 ; guix candidate
   (package
     (name "python-subprocess32")
-- 
cgit v1.2.3


From c7ca1195b9849e50ae1ac640acc4e70ff448a484 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 12 Apr 2020 15:41:08 +0300
Subject: gn: Package LMGPU and dependants

---
 gn/packages/julia.scm | 198 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 198 insertions(+)
 create mode 100644 gn/packages/julia.scm

(limited to 'gn')

diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm
new file mode 100644
index 0000000..b55efde
--- /dev/null
+++ b/gn/packages/julia.scm
@@ -0,0 +1,198 @@
+(define-module (gn packages julia)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix utils)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix git-download)
+  #:use-module (guix build-system julia)
+  #:use-module (gn packages cran)
+  #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages cran)
+  #:use-module (gnu packages statistics)
+  #:use-module (ice-9 match))
+
+(define-public julia-lmgpu
+  (let ((commit "e9e95b5fa46f1905ca1ff32a3684a2616a7e482c")
+        (revision "1"))
+    (package
+      (name "julia-lmgpu")
+      (version (git-version "0.1.1" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/ChelseaTrotter/LMGPU.jl")
+                       (commit commit)))
+                ;(file-name (git-file-name name version))
+                (file-name "LMGPU")
+                (sha256
+                 (base32
+                  "1ddx2np1lakw1l2dclpcaihxd0fcj6bjxsvaxr6g5brxjqk5j7b1"))))
+      (build-system julia-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           ;; This is a super ugly hack. Some JULIA environment variable should
+           ;; be tuned so it can find the artifact directory.
+           (add-after 'unpack 'symlink-zlib-into-artifact-directory
+             (lambda* (#:key inputs outputs #:allow-other-keys)
+               (let ((julia-dir (string-append (assoc-ref outputs "out")
+                                               "/share/julia")))
+                 (mkdir-p julia-dir)
+                 (symlink
+                   (string-append (assoc-ref inputs "julia-zlib-jll")
+                                  "/share/julia/artifacts")
+                   (string-append julia-dir "/artifacts")))
+               #t))
+           (add-after 'precompile 'check
+             (lambda* (#:key outputs #:allow-other-keys)
+               (let* ((out (assoc-ref outputs "out"))
+                      (builddir (string-append out "/share/julia/")))
+                 (setenv "JULIA_LOAD_PATH"
+                         (string-append builddir "packages/" ":"
+                                        (or (getenv "JULIA_LOAD_PATH")
+                                            "")))
+                 (setenv "HOME" (getcwd))
+                 (invoke "julia" "test/runtests.jl")))))))
+      (native-inputs
+       `(("r" ,r-minimal)
+         ("r-mice" ,r-mice)
+         ("r-qtl2" ,r-qtl2)
+         ("r-tictoc" ,r-tictoc)
+         ("r-tidyverse" ,r-tidyverse)))
+      (propagated-inputs
+       `(("julia-zipfile" ,julia-zipfile)))
+      (home-page "https://github.com/ChelseaTrotter/LMGPU.jl")
+      (synopsis "")
+      (description "")
+      (license license:expat))))
+
+(define-public julia-lmgpu-myapp
+  (package
+    (inherit julia-lmgpu)
+    (name "julia-lmgpu-myapp")
+    (source
+      (origin (inherit (package-source julia-lmgpu))
+              (file-name "MyApp")))
+    (arguments
+     (substitute-keyword-arguments (package-arguments julia-lmgpu)
+       ((#:phases phases)
+        `(modify-phases ,phases
+           (add-after 'unpack 'change-directory
+             (lambda _
+               (chdir "bin/MyApp") #t))))))
+    (propagated-inputs
+     `(("julia-lmgpu" ,julia-lmgpu)
+       ,@(package-propagated-inputs julia-lmgpu)))
+    (native-inputs
+     `(("julia-packagecompiler" ,julia-packagecompiler)))))
+
+(define-public julia-zipfile
+  (package
+    (name "julia-zipfile")
+    (version "0.9.1")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/fhs/ZipFile.jl")
+               (commit (string-append "v" version))))
+        ;(file-name (git-file-name name version))
+        (file-name "ZipFile")
+        (sha256
+         (base32
+          "1fpvlhfqg5kgq5vchlf8dyc73r6dzki0dz7plddc3bnr0ld00rlw"))))
+    (build-system julia-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; This is a super ugly hack. Some JULIA environment variable should
+         ;; be tuned so it can find the artifact directory.
+         (add-after 'unpack 'symlink-zlib-into-artifact-directory
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((julia-dir (string-append (assoc-ref outputs "out")
+                                             "/share/julia")))
+               (mkdir-p julia-dir)
+               (symlink
+                 (string-append (assoc-ref inputs "julia-zlib-jll")
+                                "/share/julia/artifacts")
+                 (string-append julia-dir "/artifacts")))
+             #t)))))
+    (propagated-inputs
+     `(("julia-zlib-jll" ,julia-zlib-jll)))
+    (home-page "https://github.com/fhs/ZipFile.jl")
+    (synopsis "Read/Write ZIP archives in Julia")
+    (description "This module provides support for reading and writing ZIP
+archives in Julia.")
+    (license license:expat)))
+
+(define-public julia-zlib-jll
+  (package
+    (name "julia-zlib-jll")
+    (version "1.2.11+9")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JuliaBinaryWrappers/Zlib_jll.jl")
+               (commit (string-append "Zlib-v" version))))
+        ;(file-name (git-file-name name version))
+        (file-name "Zlib_jll")
+        (sha256
+         (base32
+          "0m9n8dp4bwhkyjag1szmhz02k0bxzm4ka2ia2jh8crnd1qi8w9dz"))))
+    (build-system julia-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'symlink-zlib-into-artifact-directory
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((artifacts (string-append (assoc-ref outputs "out")
+                                             "/share/julia/artifacts")))
+               (mkdir-p artifacts)
+               (symlink
+                 (assoc-ref inputs "zlib")
+                 ;; from git-tree-sha1 in Artifacts.toml
+                 (string-append
+                   artifacts
+                   ,(match (%current-system)
+                      ("x86_64-linux" "/7846a2956a213715c2c76632f3461cef87d9d545")
+                      ("i686-linux" "/c8456cbd00982236828623bbc63f21b9b7b03821")
+                      ("armhf-linux" "/748c38025b5596a5005a87ac2b9476603cf8615b")
+                      ("aarch64-linux" "/3dd0c7cd5424c8746a1a32034ba1b10458f20b3b")
+                      (_ "/UNSUPPORTED")))))
+             #t)))))
+    (native-inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://github.com/JuliaBinaryWrappers/Zlib_jll.jl")
+    (synopsis "Autogenerated package constructed using BinaryBuilder.jl")
+    (description "This is an autogenerated package constructed using
+@url{https://github.com/JuliaPackaging/BinaryBuilder.jl, BinaryBuilder.jl}.")
+    (license license:expat)))
+
+(define-public julia-packagecompiler
+  (package
+    (name "julia-packagecompiler")
+    (version "1.1.1")
+    (source
+      (origin
+        (method git-fetch)
+        (uri (git-reference
+               (url "https://github.com/JuliaLang/PackageCompiler.jl")
+               (commit (string-append "v" version))))
+        ;(file-name (git-file-name name version))
+        (file-name "PackageCompiler")
+        (sha256
+         (base32
+          "1s9xc17i308fdpyvkz1w6qb1h7yncdr2jgk1szfvygxd6yzkv1b4"))))
+    (build-system julia-build-system)
+    (home-page "https://github.com/JuliaLang/PackageCompiler.jl")
+    (synopsis "Compile your Julia Package")
+    (description "PackageCompiler is a Julia package with two main purposes:
+@itemize
+@item Creating custom sysimages for reduced latency when working locally with
+packages that has a high startup time.
+@item Creating \"apps\" which are a bundle of files including an executable that
+can be sent and run on other machines without Julia being installed on that machine.
+@end itemize")
+    (license license:expat)))
-- 
cgit v1.2.3


From 803cef7f7e45280bdd68b1fef58f561d213245f4 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 19 Apr 2020 03:30:09 -0500
Subject: gn: Update bh20-seq-resource.

---
 gn/packages/bioinformatics.scm | 39 ++++++++++++---------------------------
 gn/packages/python.scm         | 39 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+), 27 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 09a706b..5a33929 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1232,8 +1232,8 @@ runApp(launch.browser=0, port=4206)~%\n"
         (license #f))))
 
 (define-public bh20-seq-resource
-  (let ((commit "ddabd9390d2b221786ef58a6d85200eecf82ca2f")
-        (revision "1"))
+  (let ((commit "bbca5ac9b2538e410efe3e09651f87e5573145de")
+        (revision "2"))
     (package
       (name "bh20-seq-resource")
       (version (git-version "1.0" revision commit))
@@ -1244,11 +1244,12 @@ runApp(launch.browser=0, port=4206)~%\n"
                        (commit commit)))
                 (file-name (git-file-name name version))
                 (sha256
-                 (base32 "04j8b7rz1vqczm6dlyvf1gx58idjhy0swmjbz4bm5r4zgpkps6mb"))))
+                 (base32 "1kkysjgmhp7kfb17470ik821p9djsidyqmkbjvv37jx2w9pvw31z"))))
       (build-system python-build-system)
       (inputs
        `(("python-arvados-python-client" ,python-arvados-python-client)
          ("python-flask" ,python-flask)
+         ("python-magic" ,python-magic)
          ("python-pyyaml" ,python-pyyaml)
          ("python-schema-salad" ,python-schema-salad)))
       (native-inputs
@@ -1269,25 +1270,17 @@ available to other researchers.")
 (define-public python-arvados-python-client
   (package
     (name "python-arvados-python-client")
-    (version "2.0.1")
+    (version "2.0.2")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "arvados-python-client" version))
         (sha256
          (base32
-          "1a363kdykj5jcrvh3q8wz06g6pqfnm2z48nfy64bls25pkiac1lr"))))
+          "19l4w6m5426x5k2kick630dh2jx26j16ycs2nhbfgr4cd43d29y4"))))
     (build-system python-build-system)
     (arguments
-     `(#:tests? #f  ; tests not included?
-       #:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'loosen-version-requirements
-           (lambda _
-             (substitute* "setup.py"
-               (("ruamel.yaml.*") "ruamel.yaml',\n")
-               (("pbr<1.7.0") "pbr"))
-             #t)))))
+     `(#:tests? #f))    ; tests not included?
     (propagated-inputs
      `(("python-ciso8601" ,python-ciso8601)
        ("python-future" ,python-future)
@@ -1295,13 +1288,13 @@ available to other researchers.")
        ("python-google-api-client" ,python-google-api-client)
        ("python-httplib2" ,python-httplib2)
        ("python-pycurl" ,python-pycurl)
-       ("python-ruamel.yaml" ,python-ruamel.yaml)
+       ("python-ruamel.yaml" ,python-ruamel.yaml-0.15)
        ("python-setuptools" ,python-setuptools)
        ("python-ws4py" ,python-ws4py)))
     (native-inputs
      `(("python-mock" ,python-mock)
        ("python-oauth2client" ,python-oauth2client)
-       ("python-pbr" ,python-pbr)
+       ("python-pbr" ,python-pbr-1.6.0)
        ("python-pyyaml" ,python-pyyaml)
        ("python-uritemplate" ,python-uritemplate)))
     (home-page "https://arvados.org")
@@ -1315,25 +1308,17 @@ server.")
 (define-public python-schema-salad
   (package
     (name "python-schema-salad")
-    (version "5.0.20200302192450")
+    (version "5.0.20200416112825")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "schema-salad" version))
         (sha256
          (base32
-          "14vqmfnnvpdaqpajwzi9gyjxx4y2mbgi3y5x3kwk2zqjnnadciv3"))))
+          "1pm6q266qrw4r0w0vnzhsvqgk5j8b3q61hxg99awhgpjsmcvkmsz"))))
     (build-system python-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'loosen-version-requirements
-           (lambda _
-             (substitute* "setup.py"
-               (("CacheControl.*") "CacheControl',\n"))
-             #t)))))
     (propagated-inputs
-     `(("python-cachecontrol" ,python-cachecontrol)
+     `(("python-cachecontrol" ,python-cachecontrol-0.11)
        ("python-lockfile" ,python-lockfile)
        ("python-mistune" ,python-mistune)
        ("python-rdflib" ,python-rdflib)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index e285880..8004507 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1101,3 +1101,42 @@ spreadsheets without the need for COM objects.")
 
 (define-public python2-admiral
   (package-with-python2 python-admiral))
+
+(define-public python-cachecontrol-0.11
+  (package
+    (inherit python-cachecontrol)
+    (name "python-cachecontrol")
+    (version "0.11.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "CacheControl" version))
+        (sha256
+         (base32
+          "07jsfhlbcwgqg6ayz8nznzaqg5rmxqblbzxz1qvg5wc44pcjjy4g"))))))
+
+(define-public python-ruamel.yaml-0.15
+  (package
+    (inherit python-ruamel.yaml)
+    (name "python-ruamel.yaml")
+    (version "0.15.77")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "ruamel.yaml" version))
+        (sha256
+         (base32
+          "1mhzxkkiv3xmr9izrgk78x7f1r5gi8kd5ac7z3vn7j00q1ydn6da"))))))
+
+(define-public python-pbr-1.6.0
+  (package
+    (inherit python-pbr)
+    (name "python-pbr")
+    (version "1.6.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "pbr" version))
+        (sha256
+         (base32
+          "1lg1klrczvzfan89y3bl9ykrknl3nb01vvai37fkww24apzyibjf"))))))
-- 
cgit v1.2.3


From f181f300430abc853ea32e9255f8ea8cfecedd19 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 21 Apr 2020 01:48:04 -0500
Subject: Add missing module import

---
 gn/packages/python.scm | 1 +
 1 file changed, 1 insertion(+)

(limited to 'gn')

diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 8004507..0953754 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -31,6 +31,7 @@
   #:use-module (gnu packages python-xyz)
   #:use-module (gnu packages rdf)
   #:use-module (gnu packages readline)
+  #:use-module (gnu packages serialization)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tcl)
   #:use-module (gnu packages tex)
-- 
cgit v1.2.3


From f1112e22eaa8226fd1698caf3e3ff77474c89dfe Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 21 Apr 2020 01:54:41 -0500
Subject: gn: ratspub: Update to 0.3.

Update inputs based on upstream's changes, add comments about skipped
input. Add hidden package of package-without-tests as dependency.
---
 gn/packages/ratspub.scm | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 3e5727c..2220062 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -1,12 +1,13 @@
 (define-module (gn packages ratspub)
   #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix utils)
   #:use-module (guix packages)
   #:use-module (guix git-download)
   #:use-module (guix build-system python)
   #:use-module (gnu packages admin)
   #:use-module (gnu packages bioinformatics)
   #:use-module (gn packages javascript)
-  #:use-module (gnu packages time)
+  #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
@@ -15,7 +16,7 @@
 (define-public ratspub
   (package
     (name "ratspub")
-    (version "0.2.2")
+    (version "0.3")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -24,10 +25,10 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "0q111fsch69kjv96d0pld9agqpwazh9p47vsvig63hmmjp72wa84"))))
+                "08z1yr1k5wddpxwdr3caqi113jx6vy38fam7k8v40sj5chv2h3b2"))))
     (build-system python-build-system)
     (arguments
-     `(#:tests? #f ; no test suite
+     `(#:tests? #f  ; no test suite
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
@@ -106,16 +107,16 @@
      `(("edirect" ,edirect)
        ("inetutils" ,inetutils)
        ("python-bcrypt" ,python-bcrypt)
-       ("python-flask" ,python-flask)
        ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+       ("python-keras" ,python-keras-for-ratspub)
        ("python-nltk" ,python-nltk)
-       ("python-pytz" ,python-pytz)))
+       ("tensorflow" ,tensorflow)))
     (native-inputs
      `(("bootstrap" ,web-bootstrap)
        ("cytoscape" ,javascript-cytoscape)
        ("font-awesome" ,web-font-awesome)
        ("jquery" ,web-jquery)
-       ;("js-popper" ,js-popper)
+       ;("js-popper" ,js-popper)    ; empty output
        ))
     (home-page "http://rats.pub/")
     (synopsis "Relationship with Addiction Through Searches of PubMed")
@@ -128,3 +129,14 @@ the question \"What do we know about these genes and addiction?\".  Data from
 Studies} catalog are also included in the search to better answer this
 question.")
     (license license:expat)))
+
+;; We want a copy of python-keras without tests.
+(define-public python-keras-for-ratspub
+  (hidden-package
+    (package
+      (inherit python-keras)
+      (arguments
+       (substitute-keyword-arguments (package-arguments python-keras)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (delete 'check))))))))
-- 
cgit v1.2.3


From 40b410c5cd5368910416df411764342d549bd770 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 21 Apr 2020 04:45:02 -0500
Subject: gn: python-rdflib-jsonld: Update to 0.5.0.

---
 gn/packages/python.scm | 23 ++++++++---------------
 1 file changed, 8 insertions(+), 15 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 0953754..c343815 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -308,30 +308,23 @@ until a value is returned.")
 (define-public python-rdflib-jsonld ; guix ready
   (package
     (name "python-rdflib-jsonld")
-    (version "0.4.0")
+    (version "0.5.0")
     (source
       (origin
         (method url-fetch)
         (uri (pypi-uri "rdflib-jsonld" version))
         (sha256
           (base32
-            "0bdw2pbjmpy1l4p6slsjn54bqy6crk5hk4san84xxirgd9w78iql"))))
+            "1v85f4hdlrrk0l1najmqmm79ijrvcj259kwsrrxiq1q5chr5azag"))))
     (build-system python-build-system)
-    (inputs
-      `(("python-setuptools" ,python-setuptools)))
+    (native-inputs
+     `(("python-nose" ,python-nose)))
     (propagated-inputs
-     `(("python-rdflib" ,python-rdflib)
-       ("python-isodate" ,python-isodate)
-       ("python-pyparsing" ,python-pyparsing)
-       ("python-html5lib" ,python-html5lib)
-       ("python-nose" ,python-nose)
-))
-    (home-page
-      "https://github.com/RDFLib/rdflib-jsonld")
-    (synopsis
-      "rdflib extension adding JSON-LD parser and serializer")
+     `(("python-rdflib" ,python-rdflib)))
+    (home-page "https://github.com/RDFLib/rdflib-jsonld")
+    (synopsis "rdflib extension adding JSON-LD parser and serializer")
     (description
-      "rdflib extension adding JSON-LD parser and serializer")
+     "This package provides an rdflib extension adding JSON-LD parser and serializer.")
     (license license:bsd-3)))
 
 (define-public python2-rdflib-jsonld
-- 
cgit v1.2.3


From 6d3d3b3d166d823fab62187ffe454bb167ccd8a8 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 21 Apr 2020 04:48:44 -0500
Subject: rearrange and deduplicate some packages

---
 gn/packages/bioinformatics.scm | 75 ----------------------------------------
 gn/packages/cwl.scm            | 77 +-----------------------------------------
 gn/packages/python.scm         | 75 ++++++++++++++++++++++++++++++++++++++++
 3 files changed, 76 insertions(+), 151 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 5a33929..02ac1e8 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1266,78 +1266,3 @@ COVID-19 Virtual Biohackathon's Public Sequence Resource project.  You can use
 it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely
 available to other researchers.")
       (license license:asl2.0))))
-
-(define-public python-arvados-python-client
-  (package
-    (name "python-arvados-python-client")
-    (version "2.0.2")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "arvados-python-client" version))
-        (sha256
-         (base32
-          "19l4w6m5426x5k2kick630dh2jx26j16ycs2nhbfgr4cd43d29y4"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f))    ; tests not included?
-    (propagated-inputs
-     `(("python-ciso8601" ,python-ciso8601)
-       ("python-future" ,python-future)
-       ;("python-google-api-python-client" ,python-google-api-python-client)
-       ("python-google-api-client" ,python-google-api-client)
-       ("python-httplib2" ,python-httplib2)
-       ("python-pycurl" ,python-pycurl)
-       ("python-ruamel.yaml" ,python-ruamel.yaml-0.15)
-       ("python-setuptools" ,python-setuptools)
-       ("python-ws4py" ,python-ws4py)))
-    (native-inputs
-     `(("python-mock" ,python-mock)
-       ("python-oauth2client" ,python-oauth2client)
-       ("python-pbr" ,python-pbr-1.6.0)
-       ("python-pyyaml" ,python-pyyaml)
-       ("python-uritemplate" ,python-uritemplate)))
-    (home-page "https://arvados.org")
-    (synopsis "Arvados client library")
-    (description "This package provides the arvados module, an API client for
-Arvados.  It also includes higher-level functions to help you write Crunch
-scripts, and command-line tools to store and retrieve data in the Keep storage
-server.")
-    (license license:asl2.0)))
-
-(define-public python-schema-salad
-  (package
-    (name "python-schema-salad")
-    (version "5.0.20200416112825")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "schema-salad" version))
-        (sha256
-         (base32
-          "1pm6q266qrw4r0w0vnzhsvqgk5j8b3q61hxg99awhgpjsmcvkmsz"))))
-    (build-system python-build-system)
-    (propagated-inputs
-     `(("python-cachecontrol" ,python-cachecontrol-0.11)
-       ("python-lockfile" ,python-lockfile)
-       ("python-mistune" ,python-mistune)
-       ("python-rdflib" ,python-rdflib)
-       ("python-rdflib-jsonld" ,python-rdflib-jsonld)
-       ("python-requests" ,python-requests)
-       ("python-ruamel.yaml" ,python-ruamel.yaml)
-       ("python-setuptools" ,python-setuptools)
-       ("python-typing-extensions" ,python-typing-extensions)))
-    (native-inputs
-     `(("python-pytest" ,python-pytest)
-       ("python-pytest-runner" ,python-pytest-runner)))
-    (home-page "https://github.com/common-workflow-language/schema_salad")
-    (synopsis "Schema Annotations for Linked Avro Data (SALAD)")
-    (description
-     "Salad is a schema language for describing JSON or YAML structured linked
-data documents.  Salad schema describes rules for preprocessing, structural
-validation, and hyperlink checking for documents described by a Salad schema.
-Salad supports rich data modeling with inheritance, template specialization,
-object identifiers, object references, documentation generation, code
-generation, and transformation to RDF.  Salad provides a bridge between document
-and record oriented data modeling and the Semantic Web.")
-    (license license:asl2.0)))
diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm
index 6e0c909..be531f6 100644
--- a/gn/packages/cwl.scm
+++ b/gn/packages/cwl.scm
@@ -61,7 +61,7 @@
        ("python-mock" ,python-mock)
        ("python-subprocess32" ,python-subprocess32)
        ("python-ruamel.yaml" ,python-ruamel.yaml)
-       ("python-cachecontrol" ,python-cachecontrol)
+       ("python-cachecontrol" ,python-cachecontrol-0.11)
        ("python-lxml" ,python-lxml)
        ("python-mypy-extensions" ,python-mypy-extensions)
        ("python-mistune" ,python-mistune)
@@ -89,78 +89,3 @@
     (description
       "Common workflow language reference implementation")
     (license license:asl2.0))))
-
-(define-public python-cachecontrol
-  (package
-    (name "python-cachecontrol")
-    (version "0.11.7")
-    (source
-     (origin
-       (method url-fetch)
-       ;; Pypi does not have tests.
-       (uri (string-append
-             "https://github.com/ionrock/cachecontrol/archive/v"
-             version ".tar.gz"))
-       (file-name (string-append name "-" version ".tar.gz"))
-       (sha256
-        (base32
-         "1yfhwihx1b1xjsx0r19va2m0r2s91im03x4d7pwzp87368f2lkkp"))))
-    (build-system python-build-system)
-    (arguments
-     `(#:tests? #f)) ;; Recent version breaks on cherrypy
-    (native-inputs
-     `(("python-pytest" ,python-pytest)
-       ("python-redis" ,python-redis)
-       ("python-webtest" ,python-webtest)
-       ("python-mock" ,python-mock)))
-    (propagated-inputs
-     `(("python-requests" ,python-requests)
-       ("python-lockfile" ,python-lockfile)))
-    (home-page "https://github.com/ionrock/cachecontrol")
-    (synopsis "The httplib2 caching algorithms for use with requests")
-    (description "CacheControl is a port of the caching algorithms in
-@code{httplib2} for use with @code{requests} session objects.")
-    (license license:asl2.0)))
-
-
-(define-public python-schema-salad
-  (let ((commit "eb85c3d49b99b7643e8a12248e2dc05504910c1e"))
-  (package
-    (name "python-schema-salad")
-    (version "3.0.20181129082112")
-    (source
-      (origin
-        ; (method url-fetch)
-        ; (uri (pypi-uri "schema-salad" version))
-       (method git-fetch)
-       (uri (git-reference
-             (url "https://github.com/genenetwork/schema_salad.git") ;; my repo for Python3.7
-             (commit commit)))
-       (file-name (git-file-name name (string-append version "-" (string-take commit 7))))
-       (sha256
-        (base32
-         "174f224zzjr0nbjlq3ypciyfijnibasysrgjswvx8yhan2dizlhr"))))
-    (build-system python-build-system)
-    (arguments `(#:tests? #f)) ;; CWL includes no tests.
-    (inputs
-      `(("python-cython" ,python-cython)
-       ("python-setuptools" ,python-setuptools)
-       ("python-rdflib-jsonld" ,python-rdflib-jsonld)
-       ("python-mistune" ,python-mistune)))
-    (propagated-inputs
-     `(("python-rdflib" ,python-rdflib)
-       ("python-avro" ,python-avro)
-       ("python-pyyaml" ,python-pyyaml)
-       ("python-requests" ,python-requests)
-       ("python-shellescape" ,python-shellescape)
-       ))
-    (home-page
-      "https://github.com/common-workflow-language/common-workflow-language")
-    (synopsis
-      "Schema Annotations for Linked Avro Data (SALAD)")
-    (description
-      "Schema Annotations for Linked Avro Data (SALAD)")
-    (license license:asl2.0))))
-
-; (define-public python2-schema-salad
-;  (package-with-python2 python-schema-salad))
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index c343815..46122ce 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -1134,3 +1134,78 @@ spreadsheets without the need for COM objects.")
         (sha256
          (base32
           "1lg1klrczvzfan89y3bl9ykrknl3nb01vvai37fkww24apzyibjf"))))))
+
+(define-public python-arvados-python-client
+  (package
+    (name "python-arvados-python-client")
+    (version "2.0.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "arvados-python-client" version))
+        (sha256
+         (base32
+          "19l4w6m5426x5k2kick630dh2jx26j16ycs2nhbfgr4cd43d29y4"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f))    ; tests not included?
+    (propagated-inputs
+     `(("python-ciso8601" ,python-ciso8601)
+       ("python-future" ,python-future)
+       ;("python-google-api-python-client" ,python-google-api-python-client)
+       ("python-google-api-client" ,python-google-api-client)
+       ("python-httplib2" ,python-httplib2)
+       ("python-pycurl" ,python-pycurl)
+       ("python-ruamel.yaml" ,python-ruamel.yaml-0.15)
+       ("python-setuptools" ,python-setuptools)
+       ("python-ws4py" ,python-ws4py)))
+    (native-inputs
+     `(("python-mock" ,python-mock)
+       ("python-oauth2client" ,python-oauth2client)
+       ("python-pbr" ,python-pbr-1.6.0)
+       ("python-pyyaml" ,python-pyyaml)
+       ("python-uritemplate" ,python-uritemplate)))
+    (home-page "https://arvados.org")
+    (synopsis "Arvados client library")
+    (description "This package provides the arvados module, an API client for
+Arvados.  It also includes higher-level functions to help you write Crunch
+scripts, and command-line tools to store and retrieve data in the Keep storage
+server.")
+    (license license:asl2.0)))
+
+(define-public python-schema-salad
+  (package
+    (name "python-schema-salad")
+    (version "5.0.20200416112825")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (pypi-uri "schema-salad" version))
+        (sha256
+         (base32
+          "1pm6q266qrw4r0w0vnzhsvqgk5j8b3q61hxg99awhgpjsmcvkmsz"))))
+    (build-system python-build-system)
+    (propagated-inputs
+     `(("python-cachecontrol" ,python-cachecontrol-0.11)
+       ("python-lockfile" ,python-lockfile)
+       ("python-mistune" ,python-mistune)
+       ("python-rdflib" ,python-rdflib)
+       ("python-rdflib-jsonld" ,python-rdflib-jsonld)
+       ("python-requests" ,python-requests)
+       ("python-ruamel.yaml" ,python-ruamel.yaml)
+       ("python-setuptools" ,python-setuptools)
+       ("python-typing-extensions" ,python-typing-extensions)))
+    (native-inputs
+     `(("python-pytest" ,python-pytest)
+       ("python-pytest-runner" ,python-pytest-runner)))
+    (home-page "https://github.com/common-workflow-language/schema_salad")
+    (synopsis "Schema Annotations for Linked Avro Data (SALAD)")
+    (description
+     "Salad is a schema language for describing JSON or YAML structured linked
+data documents.  Salad schema describes rules for preprocessing, structural
+validation, and hyperlink checking for documents described by a Salad schema.
+Salad supports rich data modeling with inheritance, template specialization,
+object identifiers, object references, documentation generation, code
+generation, and transformation to RDF.  Salad provides a bridge between document
+and record oriented data modeling and the Semantic Web.")
+    (license license:asl2.0)))
-- 
cgit v1.2.3


From cf08f2ce3485511204d984dd2eeb457675de05b0 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 21 Apr 2020 04:52:32 -0500
Subject: gn: python-rdflib-jsonld upstreamed.

---
 gn/packages/python.scm | 26 --------------------------
 1 file changed, 26 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 46122ce..7e4786f 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -305,32 +305,6 @@ until a value is returned.")
 (define-public python2-xlsxwriter
   (package-with-python2 python-xlsxwriter))
 
-(define-public python-rdflib-jsonld ; guix ready
-  (package
-    (name "python-rdflib-jsonld")
-    (version "0.5.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "rdflib-jsonld" version))
-        (sha256
-          (base32
-            "1v85f4hdlrrk0l1najmqmm79ijrvcj259kwsrrxiq1q5chr5azag"))))
-    (build-system python-build-system)
-    (native-inputs
-     `(("python-nose" ,python-nose)))
-    (propagated-inputs
-     `(("python-rdflib" ,python-rdflib)))
-    (home-page "https://github.com/RDFLib/rdflib-jsonld")
-    (synopsis "rdflib extension adding JSON-LD parser and serializer")
-    (description
-     "This package provides an rdflib extension adding JSON-LD parser and serializer.")
-    (license license:bsd-3)))
-
-(define-public python2-rdflib-jsonld
-  (package-with-python2 python-rdflib-jsonld))
-
-
 (define-public python-rserve
   (package
    (name "python-rserve")
-- 
cgit v1.2.3


From e88085103b2736000339cbef7d3c60d4bf52e3b1 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Wed, 22 Apr 2020 09:46:05 -0500
Subject: gn: update ratspub to 0.3.1.

---
 gn/packages/ratspub.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 2220062..882a6bd 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -16,7 +16,7 @@
 (define-public ratspub
   (package
     (name "ratspub")
-    (version "0.3")
+    (version "0.3.1")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -25,7 +25,7 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "08z1yr1k5wddpxwdr3caqi113jx6vy38fam7k8v40sj5chv2h3b2"))))
+                "1ii3721mqd3dbpjkhqi7yqjd9bqcf0g19kdbb8265pmbfjjsg164"))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f  ; no test suite
-- 
cgit v1.2.3


From c0c6263202917faf8af65d734724e2179db5e130 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Thu, 23 Apr 2020 09:22:53 -0500
Subject: gn: Fix ratspub python error.

We are using an older version of python-keras and tensorflow
and therefore need to backport the AUC optimizations from 2.3.1
---
 gn/packages/ratspub.scm   |   19 +-
 keras-auc-optimizer.patch | 1133 +++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 1150 insertions(+), 2 deletions(-)
 create mode 100644 keras-auc-optimizer.patch

(limited to 'gn')

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 882a6bd..9dd9745 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -1,6 +1,7 @@
 (define-module (gn packages ratspub)
   #:use-module ((guix licenses) #:prefix license:)
   #:use-module (guix utils)
+  #:use-module (gnu packages)
   #:use-module (guix packages)
   #:use-module (guix git-download)
   #:use-module (guix build-system python)
@@ -25,7 +26,15 @@
               (file-name (git-file-name name version))
               (sha256
                (base32
-                "1ii3721mqd3dbpjkhqi7yqjd9bqcf0g19kdbb8265pmbfjjsg164"))))
+                "1ii3721mqd3dbpjkhqi7yqjd9bqcf0g19kdbb8265pmbfjjsg164"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin (substitute* "server.py"
+                         ;; Keep the service running on port 4200
+                         (("4201") "4200")
+                         ;; Backport to python-keras-2.2.4
+                         (("learning_rate") "lr") )
+                       #t))))
     (build-system python-build-system)
     (arguments
      `(#:tests? #f  ; no test suite
@@ -130,11 +139,17 @@ Studies} catalog are also included in the search to better answer this
 question.")
     (license license:expat)))
 
-;; We want a copy of python-keras without tests.
+;; We want a copy of python-keras with the AUC optimizer backported.
+;; We skip the tests because we "test in production".
+;; That's a lie. The test suite just takes a long time to run.
 (define-public python-keras-for-ratspub
   (hidden-package
     (package
       (inherit python-keras)
+      (source
+        (origin
+          (inherit (package-source python-keras))
+          (patches (search-patches "keras-auc-optimizer.patch"))))
       (arguments
        (substitute-keyword-arguments (package-arguments python-keras)
          ((#:phases phases)
diff --git a/keras-auc-optimizer.patch b/keras-auc-optimizer.patch
new file mode 100644
index 0000000..bbc6924
--- /dev/null
+++ b/keras-auc-optimizer.patch
@@ -0,0 +1,1133 @@
+From 901159da45695da24a5206125910f02fc50169ce Mon Sep 17 00:00:00 2001
+From: Efraim Flashner <efraim@flashner.co.il>
+Date: Thu, 23 Apr 2020 15:50:37 +0300
+Subject: [PATCH] add keras metrics
+
+---
+ keras/backend/tensorflow_backend.py |  12 +
+ keras/metrics.py                    | 584 ++++++++++++++++++++++++++++
+ keras/utils/__init__.py             |   2 +
+ keras/utils/losses_utils.py         | 177 +++++++++
+ keras/utils/metrics_utils.py        | 278 +++++++++++++
+ 5 files changed, 1053 insertions(+)
+ create mode 100644 keras/utils/losses_utils.py
+ create mode 100644 keras/utils/metrics_utils.py
+
+diff --git a/keras/backend/tensorflow_backend.py b/keras/backend/tensorflow_backend.py
+index bcb8be0..a2870f5 100644
+--- a/keras/backend/tensorflow_backend.py
++++ b/keras/backend/tensorflow_backend.py
+@@ -4453,3 +4453,15 @@ def local_conv2d(inputs, kernel, kernel_size, strides, output_shape, data_format
+     else:
+         output = permute_dimensions(output, (2, 0, 1, 3))
+     return output
++
++#get_graph = tf_keras_backend.get_graph
++
++#def is_symbolic(x):
++#    return isinstance(x, tf.Tensor) and hasattr(x, 'op')
++
++def size(x, name=None):
++#    if is_symbolic(x):
++#        with get_graph().as_default():
++#            return tf.size(x)
++    return tf.size(x, name=name)
++
+diff --git a/keras/metrics.py b/keras/metrics.py
+index 8e3df1f..8f57910 100644
+--- a/keras/metrics.py
++++ b/keras/metrics.py
+@@ -4,8 +4,12 @@ from __future__ import absolute_import
+ from __future__ import division
+ from __future__ import print_function
+ 
++import abc
+ import six
++import types
++
+ from . import backend as K
++from .engine.base_layer import Layer
+ from .losses import mean_squared_error
+ from .losses import mean_absolute_error
+ from .losses import mean_absolute_percentage_error
+@@ -19,10 +23,201 @@ from .losses import binary_crossentropy
+ from .losses import kullback_leibler_divergence
+ from .losses import poisson
+ from .losses import cosine_proximity
++from .utils import losses_utils
++from .utils import metrics_utils
+ from .utils.generic_utils import deserialize_keras_object
+ from .utils.generic_utils import serialize_keras_object
+ 
+ 
++@six.add_metaclass(abc.ABCMeta)
++class Metric(Layer):
++    """Encapsulates metric logic and state.
++
++    Standalone usage:
++    ```python
++    m = SomeMetric(...)
++    for input in ...:
++        m.update_state(input)
++    m.result()
++    ```
++
++    Usage with the `compile` API:
++    ```python
++    model.compile(optimizer='rmsprop',
++                  loss=keras.losses.categorical_crossentropy,
++                  metrics=[keras.metrics.CategoricalAccuracy()])
++    ```
++
++    To be implemented by subclasses:
++    * `__init__()`: All state variables should be created in this method by
++        calling `self.add_weight()` like: `self.var = self.add_weight(...)`
++    * `update_state()`: Has all updates to the state variables like:
++        self.var.assign_add(...).
++    * `result()`: Computes and returns a value for the metric
++        from the state variables.
++    """
++
++    def __init__(self, name=None, dtype=None, **kwargs):
++        super(Metric, self).__init__(name=name, dtype=dtype, **kwargs)
++        self.stateful = True  # All metric layers are stateful.
++        self.built = True
++        self.dtype = K.floatx() if dtype is None else dtype
++
++    def __new__(cls, *args, **kwargs):
++        obj = super(Metric, cls).__new__(cls)
++        update_state_fn = obj.update_state
++
++        obj.update_state = types.MethodType(
++            metrics_utils.update_state_wrapper(update_state_fn), obj)
++        return obj
++
++    def __call__(self, *args, **kwargs):
++        """Accumulates statistics and then computes metric result value."""
++        update_op = self.update_state(*args, **kwargs)
++        return self.result()
++
++    def get_config(self):
++        """Returns the serializable config of the metric."""
++        return {'name': self.name, 'dtype': self.dtype}
++
++    def reset_states(self):
++        """Resets all of the metric state variables.
++        This function is called between epochs/steps,
++        when a metric is evaluated during training.
++        """
++        K.batch_set_value([(v, 0) for v in self.weights])
++
++    @abc.abstractmethod
++    def update_state(self, *args, **kwargs):
++        """Accumulates statistics for the metric. """
++        raise NotImplementedError('Must be implemented in subclasses.')
++
++    @abc.abstractmethod
++    def result(self):
++        """Computes and returns the metric value tensor.
++        Result computation is an idempotent operation that simply calculates the
++        metric value using the state variables.
++        """
++        raise NotImplementedError('Must be implemented in subclasses.')
++
++    # For use by subclasses #
++    def add_weight(self,
++                   name,
++                   shape=(),
++                   initializer=None,
++                   dtype=None):
++        """Adds state variable. Only for use by subclasses."""
++        return super(Metric, self).add_weight(
++            name=name,
++            shape=shape,
++            dtype=self.dtype if dtype is None else dtype,
++            trainable=False,
++            initializer=initializer)
++
++    # End: For use by subclasses ###
++
++
++class Reduce(Metric):
++    """Encapsulates metrics that perform a reduce operation on the values."""
++
++    def __init__(self, reduction, name, dtype=None):
++        """Creates a `Reduce` instance.
++        # Arguments
++            reduction: a metrics `Reduction` enum value.
++            name: string name of the metric instance.
++            dtype: (Optional) data type of the metric result.
++        """
++        super(Reduce, self).__init__(name=name, dtype=dtype)
++        self.reduction = reduction
++        self.total = self.add_weight('total', initializer='zeros')
++        if reduction in [metrics_utils.Reduction.SUM_OVER_BATCH_SIZE,
++                         metrics_utils.Reduction.WEIGHTED_MEAN]:
++            self.count = self.add_weight('count', initializer='zeros')
++
++    def update_state(self, values, sample_weight=None):
++        """Accumulates statistics for computing the reduction metric.
++        For example, if `values` is [1, 3, 5, 7] and reduction=SUM_OVER_BATCH_SIZE,
++        then the value of `result()` is 4. If the `sample_weight` is specified as
++        [1, 1, 0, 0] then value of `result()` would be 2.
++        # Arguments
++            values: Per-example value.
++            sample_weight: Optional weighting of each example. Defaults to 1.
++        """
++        values = K.cast(values, self.dtype)
++        if sample_weight is not None:
++            sample_weight = K.cast(sample_weight, self.dtype)
++            # Update dimensions of weights to match with values if possible.
++            values, _, sample_weight = losses_utils.squeeze_or_expand_dimensions(
++                values, sample_weight=sample_weight)
++
++            # Broadcast weights if possible.
++            sample_weight = losses_utils.broadcast_weights(sample_weight, values)
++            values = values * sample_weight
++
++        value_sum = K.sum(values)
++        update_total_op = K.update_add(self.total, value_sum)
++
++        # Exit early if the reduction doesn't have a denominator.
++        if self.reduction == metrics_utils.Reduction.SUM:
++            return update_total_op
++
++        # Update `count` for reductions that require a denominator.
++        if self.reduction == metrics_utils.Reduction.SUM_OVER_BATCH_SIZE:
++            num_values = K.cast(K.size(values), self.dtype)
++        elif self.reduction == metrics_utils.Reduction.WEIGHTED_MEAN:
++            if sample_weight is None:
++                num_values = K.cast(K.size(values), self.dtype)
++            else:
++                num_values = K.sum(sample_weight)
++        else:
++            raise NotImplementedError(
++                'reduction [%s] not implemented' % self.reduction)
++
++        with K.control_dependencies([update_total_op]):
++            return K.update_add(self.count, num_values)
++
++    def result(self):
++        if self.reduction == metrics_utils.Reduction.SUM:
++            return self.total
++        elif self.reduction in [
++            metrics_utils.Reduction.WEIGHTED_MEAN,
++            metrics_utils.Reduction.SUM_OVER_BATCH_SIZE
++        ]:
++            return self.total / self.count
++        else:
++            raise NotImplementedError(
++                'reduction [%s] not implemented' % self.reduction)
++
++
++class Sum(Reduce):
++    """Computes the (weighted) sum of the given values.
++
++    For example, if values is [1, 3, 5, 7] then the sum is 16.
++    If the weights were specified as [1, 1, 0, 0] then the sum would be 4.
++
++    This metric creates one variable, `total`, that is used to compute the sum of
++    `values`. This is ultimately returned as `sum`.
++    If `sample_weight` is `None`, weights default to 1.  Use `sample_weight` of 0
++    to mask values.
++
++    Standalone usage:
++    ```python
++    m = keras.metrics.Sum()
++    m.update_state([1, 3, 5, 7])
++    m.result()
++    ```
++    """
++
++    def __init__(self, name='sum', dtype=None):
++        """Creates a `Sum` instance.
++        # Arguments
++            name: (Optional) string name of the metric instance.
++            dtype: (Optional) data type of the metric result.
++        """
++        super(Sum, self).__init__(reduction=metrics_utils.Reduction.SUM,
++                                  name=name, dtype=dtype)
++
++
+ def binary_accuracy(y_true, y_pred):
+     return K.mean(K.equal(y_true, K.round(y_pred)), axis=-1)
+ 
+@@ -49,6 +244,395 @@ def sparse_top_k_categorical_accuracy(y_true, y_pred, k=5):
+     return K.mean(K.in_top_k(y_pred, K.cast(K.flatten(y_true), 'int32'), k),
+                   axis=-1)
+ 
++class SensitivitySpecificityBase(Metric):
++    """Abstract base class for computing sensitivity and specificity.
++
++    For additional information about specificity and sensitivity, see the
++    following: https://en.wikipedia.org/wiki/Sensitivity_and_specificity
++    """
++
++    def __init__(self, value, num_thresholds=200, name=None, dtype=None):
++        super(SensitivitySpecificityBase, self).__init__(name=name, dtype=dtype)
++        if num_thresholds <= 0:
++            raise ValueError('`num_thresholds` must be > 0.')
++        self.value = value
++        self.true_positives = self.add_weight(
++            'true_positives',
++            shape=(num_thresholds,),
++            initializer='zeros')
++        self.true_negatives = self.add_weight(
++            'true_negatives',
++            shape=(num_thresholds,),
++            initializer='zeros')
++        self.false_positives = self.add_weight(
++            'false_positives',
++            shape=(num_thresholds,),
++            initializer='zeros')
++        self.false_negatives = self.add_weight(
++            'false_negatives',
++            shape=(num_thresholds,),
++            initializer='zeros')
++
++        # Compute `num_thresholds` thresholds in [0, 1]
++        if num_thresholds == 1:
++            self.thresholds = [0.5]
++        else:
++            thresholds = [(i + 1) * 1.0 / (num_thresholds - 1)
++                          for i in range(num_thresholds - 2)]
++            self.thresholds = [0.0] + thresholds + [1.0]
++
++    def update_state(self, y_true, y_pred, sample_weight=None):
++        return metrics_utils.update_confusion_matrix_variables(
++            {
++                metrics_utils.ConfusionMatrix.TRUE_POSITIVES: self.true_positives,
++                metrics_utils.ConfusionMatrix.TRUE_NEGATIVES: self.true_negatives,
++                metrics_utils.ConfusionMatrix.FALSE_POSITIVES: self.false_positives,
++                metrics_utils.ConfusionMatrix.FALSE_NEGATIVES: self.false_negatives,
++            },
++            y_true,
++            y_pred,
++            thresholds=self.thresholds,
++            sample_weight=sample_weight)
++
++    def reset_states(self):
++        num_thresholds = len(self.thresholds)
++        K.batch_set_value(
++            [(v, np.zeros((num_thresholds,))) for v in self.variables])
++
++
++class SensitivityAtSpecificity(SensitivitySpecificityBase):
++    """Computes the sensitivity at a given specificity.
++
++    `Sensitivity` measures the proportion of actual positives that are correctly
++    identified as such (tp / (tp + fn)).
++    `Specificity` measures the proportion of actual negatives that are correctly
++    identified as such (tn / (tn + fp)).
++
++    This metric creates four local variables, `true_positives`, `true_negatives`,
++    `false_positives` and `false_negatives` that are used to compute the
++    sensitivity at the given specificity. The threshold for the given specificity
++    value is computed and used to evaluate the corresponding sensitivity.
++
++    If `sample_weight` is `None`, weights default to 1.
++    Use `sample_weight` of 0 to mask values.
++
++    For additional information about specificity and sensitivity, see the
++    following: https://en.wikipedia.org/wiki/Sensitivity_and_specificity
++
++    Usage with the compile API:
++
++    ```python
++    model = keras.Model(inputs, outputs)
++    model.compile(
++        'sgd',
++        loss='mse',
++        metrics=[keras.metrics.SensitivityAtSpecificity()])
++    ```
++
++    # Arguments
++        specificity: A scalar value in range `[0, 1]`.
++        num_thresholds: (Optional) Defaults to 200. The number of thresholds to
++            use for matching the given specificity.
++        name: (Optional) string name of the metric instance.
++        dtype: (Optional) data type of the metric result.
++    """
++
++    def __init__(self, specificity, num_thresholds=200, name=None, dtype=None):
++        if specificity < 0 or specificity > 1:
++            raise ValueError('`specificity` must be in the range [0, 1].')
++        self.specificity = specificity
++        self.num_thresholds = num_thresholds
++        super(SensitivityAtSpecificity, self).__init__(
++            specificity, num_thresholds=num_thresholds, name=name, dtype=dtype)
++
++    def result(self):
++        # Calculate specificities at all the thresholds.
++        specificities = K.switch(
++            K.greater(self.true_negatives + self.false_positives, 0),
++            (self.true_negatives / (self.true_negatives + self.false_positives)),
++            K.zeros_like(self.thresholds))
++
++        # Find the index of the threshold where the specificity is closest to the
++        # given specificity.
++        min_index = K.argmin(
++            K.abs(specificities - self.value), axis=0)
++        min_index = K.cast(min_index, 'int32')
++
++        # Compute sensitivity at that index.
++        return K.switch(
++            K.greater((self.true_positives[min_index] +
++                       self.false_negatives[min_index]), 0),
++            (self.true_positives[min_index] /
++                (self.true_positives[min_index] + self.false_negatives[min_index])),
++            K.zeros_like(self.true_positives[min_index]))
++
++    def get_config(self):
++        config = {
++            'num_thresholds': self.num_thresholds,
++            'specificity': self.specificity
++        }
++        base_config = super(SensitivityAtSpecificity, self).get_config()
++        return dict(list(base_config.items()) + list(config.items()))
++
++
++class AUC(Metric):
++    """Computes the approximate AUC (Area under the curve) via a Riemann sum.
++
++    This metric creates four local variables, `true_positives`, `true_negatives`,
++    `false_positives` and `false_negatives` that are used to compute the AUC.
++    To discretize the AUC curve, a linearly spaced set of thresholds is used to
++    compute pairs of recall and precision values. The area under the ROC-curve is
++    therefore computed using the height of the recall values by the false positive
++    rate, while the area under the PR-curve is the computed using the height of
++    the precision values by the recall.
++
++    This value is ultimately returned as `auc`, an idempotent operation that
++    computes the area under a discretized curve of precision versus recall values
++    (computed using the aforementioned variables). The `num_thresholds` variable
++    controls the degree of discretization with larger numbers of thresholds more
++    closely approximating the true AUC. The quality of the approximation may vary
++    dramatically depending on `num_thresholds`. The `thresholds` parameter can be
++    used to manually specify thresholds which split the predictions more evenly.
++
++    For best results, `predictions` should be distributed approximately uniformly
++    in the range [0, 1] and not peaked around 0 or 1. The quality of the AUC
++    approximation may be poor if this is not the case. Setting `summation_method`
++    to 'minoring' or 'majoring' can help quantify the error in the approximation
++    by providing lower or upper bound estimate of the AUC.
++
++    If `sample_weight` is `None`, weights default to 1.
++    Use `sample_weight` of 0 to mask values.
++
++    Usage with the compile API:
++
++    ```python
++    model = keras.Model(inputs, outputs)
++    model.compile('sgd', loss='mse', metrics=[keras.metrics.AUC()])
++    ```
++
++    # Arguments
++        num_thresholds: (Optional) Defaults to 200. The number of thresholds to
++            use when discretizing the roc curve. Values must be > 1.
++            curve: (Optional) Specifies the name of the curve to be computed, 'ROC'
++            [default] or 'PR' for the Precision-Recall-curve.
++        summation_method: (Optional) Specifies the Riemann summation method used
++            (https://en.wikipedia.org/wiki/Riemann_sum): 'interpolation' [default],
++              applies mid-point summation scheme for `ROC`. For PR-AUC, interpolates
++              (true/false) positives but not the ratio that is precision (see Davis
++              & Goadrich 2006 for details); 'minoring' that applies left summation
++              for increasing intervals and right summation for decreasing intervals;
++              'majoring' that does the opposite.
++        name: (Optional) string name of the metric instance.
++        dtype: (Optional) data type of the metric result.
++        thresholds: (Optional) A list of floating point values to use as the
++            thresholds for discretizing the curve. If set, the `num_thresholds`
++            parameter is ignored. Values should be in [0, 1]. Endpoint thresholds
++            equal to {-epsilon, 1+epsilon} for a small positive epsilon value will
++            be automatically included with these to correctly handle predictions
++            equal to exactly 0 or 1.
++    """
++
++    def __init__(self,
++                 num_thresholds=200,
++                 curve='ROC',
++                 summation_method='interpolation',
++                 name=None,
++                 dtype=None,
++                 thresholds=None):
++        # Validate configurations.
++        if (isinstance(curve, metrics_utils.AUCCurve) and
++                curve not in list(metrics_utils.AUCCurve)):
++            raise ValueError('Invalid curve: "{}". Valid options are: "{}"'.format(
++                curve, list(metrics_utils.AUCCurve)))
++        if isinstance(
++            summation_method,
++            metrics_utils.AUCSummationMethod) and summation_method not in list(
++                metrics_utils.AUCSummationMethod):
++            raise ValueError(
++                'Invalid summation method: "{}". Valid options are: "{}"'.format(
++                    summation_method, list(metrics_utils.AUCSummationMethod)))
++
++        # Update properties.
++        if thresholds is not None:
++            # If specified, use the supplied thresholds.
++            self.num_thresholds = len(thresholds) + 2
++            thresholds = sorted(thresholds)
++        else:
++            if num_thresholds <= 1:
++                raise ValueError('`num_thresholds` must be > 1.')
++
++            # Otherwise, linearly interpolate (num_thresholds - 2) thresholds in
++            # (0, 1).
++            self.num_thresholds = num_thresholds
++            thresholds = [(i + 1) * 1.0 / (num_thresholds - 1)
++                          for i in range(num_thresholds - 2)]
++
++        # Add an endpoint "threshold" below zero and above one for either
++        # threshold method to account for floating point imprecisions.
++        self.thresholds = [0.0 - K.epsilon()] + thresholds + [1.0 + K.epsilon()]
++
++        if isinstance(curve, metrics_utils.AUCCurve):
++            self.curve = curve
++        else:
++            self.curve = metrics_utils.AUCCurve.from_str(curve)
++        if isinstance(summation_method, metrics_utils.AUCSummationMethod):
++            self.summation_method = summation_method
++        else:
++            self.summation_method = metrics_utils.AUCSummationMethod.from_str(
++                summation_method)
++        super(AUC, self).__init__(name=name, dtype=dtype)
++
++        # Create metric variables
++        self.true_positives = self.add_weight(
++            'true_positives',
++            shape=(self.num_thresholds,),
++            initializer='zeros')
++        self.true_negatives = self.add_weight(
++            'true_negatives',
++            shape=(self.num_thresholds,),
++            initializer='zeros')
++        self.false_positives = self.add_weight(
++            'false_positives',
++            shape=(self.num_thresholds,),
++            initializer='zeros')
++        self.false_negatives = self.add_weight(
++            'false_negatives',
++            shape=(self.num_thresholds,),
++            initializer='zeros')
++
++    def update_state(self, y_true, y_pred, sample_weight=None):
++        return metrics_utils.update_confusion_matrix_variables({
++            metrics_utils.ConfusionMatrix.TRUE_POSITIVES: self.true_positives,
++            metrics_utils.ConfusionMatrix.TRUE_NEGATIVES: self.true_negatives,
++            metrics_utils.ConfusionMatrix.FALSE_POSITIVES: self.false_positives,
++            metrics_utils.ConfusionMatrix.FALSE_NEGATIVES: self.false_negatives,
++        }, y_true, y_pred, self.thresholds, sample_weight=sample_weight)
++
++    def interpolate_pr_auc(self):
++        """Interpolation formula inspired by section 4 of Davis & Goadrich 2006.
++
++        https://www.biostat.wisc.edu/~page/rocpr.pdf
++
++        Note here we derive & use a closed formula not present in the paper
++        as follows:
++
++          Precision = TP / (TP + FP) = TP / P
++
++        Modeling all of TP (true positive), FP (false positive) and their sum
++        P = TP + FP (predicted positive) as varying linearly within each interval
++        [A, B] between successive thresholds, we get
++
++          Precision slope = dTP / dP
++                          = (TP_B - TP_A) / (P_B - P_A)
++                          = (TP - TP_A) / (P - P_A)
++          Precision = (TP_A + slope * (P - P_A)) / P
++
++        The area within the interval is (slope / total_pos_weight) times
++
++          int_A^B{Precision.dP} = int_A^B{(TP_A + slope * (P - P_A)) * dP / P}
++          int_A^B{Precision.dP} = int_A^B{slope * dP + intercept * dP / P}
++
++        where intercept = TP_A - slope * P_A = TP_B - slope * P_B, resulting in
++
++          int_A^B{Precision.dP} = TP_B - TP_A + intercept * log(P_B / P_A)
++
++        Bringing back the factor (slope / total_pos_weight) we'd put aside, we get
++
++          slope * [dTP + intercept *  log(P_B / P_A)] / total_pos_weight
++
++        where dTP == TP_B - TP_A.
++
++        Note that when P_A == 0 the above calculation simplifies into
++
++          int_A^B{Precision.dTP} = int_A^B{slope * dTP} = slope * (TP_B - TP_A)
++
++        which is really equivalent to imputing constant precision throughout the
++        first bucket having >0 true positives.
++
++        # Returns
++            pr_auc: an approximation of the area under the P-R curve.
++        """
++        dtp = self.true_positives[:self.num_thresholds -
++                                  1] - self.true_positives[1:]
++        p = self.true_positives + self.false_positives
++        dp = p[:self.num_thresholds - 1] - p[1:]
++
++        prec_slope = dtp / K.maximum(dp, 0)
++        intercept = self.true_positives[1:] - (prec_slope * p[1:])
++
++        # Logical and
++        pMin = K.expand_dims(p[:self.num_thresholds - 1] > 0, 0)
++        pMax = K.expand_dims(p[1:] > 0, 0)
++        are_different = K.concatenate([pMin, pMax], axis=0)
++        switch_condition = K.all(are_different, axis=0)
++
++        safe_p_ratio = K.switch(
++            switch_condition,
++            p[:self.num_thresholds - 1] / K.maximum(p[1:], 0),
++            K.ones_like(p[1:]))
++
++        numer = prec_slope * (dtp + intercept * K.log(safe_p_ratio))
++        denom = K.maximum(self.true_positives[1:] + self.false_negatives[1:], 0)
++        return K.sum((numer / denom))
++
++    def result(self):
++        if (self.curve == metrics_utils.AUCCurve.PR and
++                (self.summation_method ==
++                 metrics_utils.AUCSummationMethod.INTERPOLATION)):
++            # This use case is different and is handled separately.
++            return self.interpolate_pr_auc()
++
++        # Set `x` and `y` values for the curves based on `curve` config.
++        recall = K.switch(
++            K.greater((self.true_positives), 0),
++            (self.true_positives /
++                (self.true_positives + self.false_negatives)),
++            K.zeros_like(self.true_positives))
++        if self.curve == metrics_utils.AUCCurve.ROC:
++            fp_rate = K.switch(
++                K.greater((self.false_positives), 0),
++                (self.false_positives /
++                    (self.false_positives + self.true_negatives)),
++                K.zeros_like(self.false_positives))
++            x = fp_rate
++            y = recall
++        else:  # curve == 'PR'.
++            precision = K.switch(
++                K.greater((self.true_positives), 0),
++                (self.true_positives / (self.true_positives + self.false_positives)),
++                K.zeros_like(self.true_positives))
++            x = recall
++            y = precision
++
++        # Find the rectangle heights based on `summation_method`.
++        if self.summation_method == metrics_utils.AUCSummationMethod.INTERPOLATION:
++            # Note: the case ('PR', 'interpolation') has been handled above.
++            heights = (y[:self.num_thresholds - 1] + y[1:]) / 2.
++        elif self.summation_method == metrics_utils.AUCSummationMethod.MINORING:
++            heights = K.minimum(y[:self.num_thresholds - 1], y[1:])
++        else:  # self.summation_method = metrics_utils.AUCSummationMethod.MAJORING:
++            heights = K.maximum(y[:self.num_thresholds - 1], y[1:])
++
++        # Sum up the areas of all the rectangles.
++        return K.sum((x[:self.num_thresholds - 1] - x[1:]) * heights)
++
++    def reset_states(self):
++        K.batch_set_value(
++            [(v, np.zeros((self.num_thresholds,))) for v in self.variables])
++
++    def get_config(self):
++        config = {
++            'num_thresholds': self.num_thresholds,
++            'curve': self.curve.value,
++            'summation_method': self.summation_method.value,
++            # We remove the endpoint thresholds as an inverse of how the thresholds
++            # were initialized. This ensures that a metric initialized from this
++            # config has the same thresholds.
++            'thresholds': self.thresholds[1:-1],
++        }
++        base_config = super(AUC, self).get_config()
++        return dict(list(base_config.items()) + list(config.items()))
++
+ 
+ # Aliases
+ 
+diff --git a/keras/utils/__init__.py b/keras/utils/__init__.py
+index 8cc39d5..65af329 100644
+--- a/keras/utils/__init__.py
++++ b/keras/utils/__init__.py
+@@ -4,6 +4,8 @@ from . import generic_utils
+ from . import data_utils
+ from . import io_utils
+ from . import conv_utils
++from . import losses_utils
++from . import metrics_utils
+ 
+ # Globally-importable utils.
+ from .io_utils import HDF5Matrix
+diff --git a/keras/utils/losses_utils.py b/keras/utils/losses_utils.py
+new file mode 100644
+index 0000000..617ebb7
+--- /dev/null
++++ b/keras/utils/losses_utils.py
+@@ -0,0 +1,177 @@
++"""Utilities related to losses."""
++from __future__ import absolute_import
++from __future__ import division
++from __future__ import print_function
++
++import numpy as np
++
++from .. import backend as K
++
++
++class Reduction(object):
++    """Types of loss reduction.
++
++    Contains the following values:
++
++    * `NONE`: Un-reduced weighted losses with the same shape as input. When this
++        reduction type used with built-in Keras training loops like
++        `fit`/`evaluate`, the unreduced vector loss is passed to the optimizer but
++        the reported loss will be a scalar value.
++    * `SUM`: Scalar sum of weighted losses.
++    * `SUM_OVER_BATCH_SIZE`: Scalar `SUM` divided by number of elements in losses.
++    """
++
++    NONE = 'none'
++    SUM = 'sum'
++    SUM_OVER_BATCH_SIZE = 'sum_over_batch_size'
++
++    @classmethod
++    def all(cls):
++        return (cls.NONE, cls.SUM, cls.SUM_OVER_BATCH_SIZE)
++
++    @classmethod
++    def validate(cls, key):
++        if key not in cls.all():
++            raise ValueError('Invalid Reduction Key %s.' % key)
++
++
++def squeeze_or_expand_dimensions(y_pred, y_true=None, sample_weight=None):
++    """Squeeze or expand last dimension if needed.
++
++    1. Squeezes last dim of `y_pred` or `y_true` if their rank differs by 1.
++    2. Squeezes or expands last dim of `sample_weight` if its rank differs by 1
++    from the new rank of `y_pred`.
++    If `sample_weight` is scalar, it is kept scalar.
++
++    # Arguments
++    y_pred: Predicted values, a `Tensor` of arbitrary dimensions.
++    y_true: Optional label `Tensor` whose dimensions match `y_pred`.
++    sample_weight: Optional weight scalar or `Tensor` whose dimensions match
++    `y_pred`.
++
++    # Returns
++    Tuple of `y_pred`, `y_true` and `sample_weight`. Each of them possibly has
++    the last dimension squeezed, `sample_weight` could be extended by one
++    dimension.
++    """
++    if y_true is not None:
++        y_pred_rank = K.ndim(y_pred)
++        y_pred_shape = K.int_shape(y_pred)
++        y_true_rank = K.ndim(y_true)
++        y_true_shape = K.int_shape(y_true)
++
++        if (y_pred_rank - y_true_rank == 1) and (y_pred_shape[-1] == 1):
++            y_pred = K.squeeze(y_pred, -1)
++        elif (y_true_rank - y_pred_rank == 1) and (y_true_shape[-1] == 1):
++            y_true = K.squeeze(y_true, -1)
++
++    if sample_weight is None:
++        return y_pred, y_true
++
++    y_pred_rank = K.ndim(y_pred)
++    weights_rank = K.ndim(sample_weight)
++    if weights_rank != 0:
++        if weights_rank - y_pred_rank == 1:
++            sample_weight = K.squeeze(sample_weight, -1)
++        elif y_pred_rank - weights_rank == 1:
++           sample_weight = K.expand_dims(sample_weight, -1)
++    return y_pred, y_true, sample_weight
++
++
++def _num_elements(losses):
++    """Computes the number of elements in `losses` tensor."""
++    with K.name_scope('num_elements') as scope:
++        return K.cast(K.size(losses, name=scope), losses.dtype)
++
++
++def reduce_weighted_loss(weighted_losses, reduction=Reduction.SUM_OVER_BATCH_SIZE):
++    """Reduces the individual weighted loss measurements."""
++    if reduction == Reduction.NONE:
++        loss = weighted_losses
++    else:
++        loss = K.sum(weighted_losses)
++        if reduction == Reduction.SUM_OVER_BATCH_SIZE:
++            loss = loss / _num_elements(weighted_losses)
++    return loss
++
++
++def broadcast_weights(values, sample_weight):
++    # Broadcast weights if possible.
++    weights_shape = K.int_shape(sample_weight)
++    values_shape = K.int_shape(values)
++
++    if values_shape != weights_shape:
++        weights_rank = K.ndim(sample_weight)
++        values_rank = K.ndim(values)
++
++        # Raise error if ndim of weights is > values.
++        if weights_rank > values_rank:
++            raise ValueError(
++                'Incompatible shapes: `values` {} vs `sample_weight` {}'.format(
++                    values_shape, weights_shape))
++
++        # Expand dim of weights to match ndim of values, if required.
++            for i in range(weights_rank, values_rank):
++                sample_weight = K.expand_dims(sample_weight, axis=i)
++
++        if weights_shape is not None and values_shape is not None:
++            for i in range(weights_rank):
++                if (weights_shape[i] is not None and
++                   values_shape[i] is not None and
++                       weights_shape[i] != values_shape[i]):
++                   # Cannot be broadcasted.
++                   if weights_shape[i] != 1:
++                       raise ValueError(
++                           'Incompatible shapes: `values` {} vs '
++                           '`sample_weight` {}'.format(
++                               values_shape, weights_shape))
++                   sample_weight = K.repeat_elements(
++                       sample_weight, values_shape[i], axis=i)
++    return sample_weight
++
++
++def compute_weighted_loss(losses,
++                          sample_weight=None,
++                          reduction=Reduction.SUM_OVER_BATCH_SIZE,
++                          name=None):
++    """Computes the weighted loss.
++
++    # Arguments
++        losses: `Tensor` of shape `[batch_size, d1, ... dN]`.
++        sample_weight: Optional `Tensor` whose rank is either 0, or the same rank as
++        `   losses`, or be broadcastable to `losses`.
++        reduction: (Optional) Type of Reduction to apply to loss.
++            Default value is `SUM_OVER_BATCH_SIZE`.
++        name: Optional name for the op.
++
++    # Raises
++        ValueError: If the shape of `sample_weight` is not compatible with `losses`.
++
++    # Returns
++        Weighted loss `Tensor` of the same type as `losses`. If `reduction` is
++            `NONE`, this has the same shape as `losses`; otherwise, it is scalar.
++    """
++    Reduction.validate(reduction)
++    if sample_weight is None:
++        sample_weight = 1.0
++    with K.name_scope(name or 'weighted_loss'):
++        input_dtype = K.dtype(losses)
++        losses = K.cast(losses, K.floatx())
++        sample_weight = K.cast(sample_weight, K.floatx())
++
++        # Update dimensions of `sample_weight` to match with `losses` if possible.
++        losses, _, sample_weight = squeeze_or_expand_dimensions(
++            losses, None, sample_weight)
++
++        # Broadcast weights if possible.
++        sample_weight = broadcast_weights(losses, sample_weight)
++
++        # Apply weights to losses.
++        weighted_losses = sample_weight * losses
++
++        # Apply reduction function to the individual weighted losses.
++        loss = reduce_weighted_loss(weighted_losses, reduction)
++        # Convert the result back to the input type.
++        loss = K.cast(loss, input_dtype)
++        return loss
++
+diff --git a/keras/utils/metrics_utils.py b/keras/utils/metrics_utils.py
+new file mode 100644
+index 0000000..e6a5bb0
+--- /dev/null
++++ b/keras/utils/metrics_utils.py
+@@ -0,0 +1,278 @@
++"""Utilities related to metrics."""
++from __future__ import absolute_import
++from __future__ import division
++from __future__ import print_function
++
++from enum import Enum
++
++from .. import backend as K
++from . import losses_utils
++
++NEG_INF = -1e10
++
++class Reduction(object):
++    """Types of metrics reduction.
++    Contains the following values:
++    * `SUM`: Scalar sum of weighted values.
++    * `SUM_OVER_BATCH_SIZE`: Scalar `SUM` of weighted values divided by
++        number of elements in values.
++    * `WEIGHTED_MEAN`: Scalar sum of weighted values divided by sum of weights.
++    """
++
++    SUM = 'sum'
++    SUM_OVER_BATCH_SIZE = 'sum_over_batch_size'
++    WEIGHTED_MEAN = 'weighted_mean'
++
++
++def update_state_wrapper(update_state_fn):
++    """Decorator to wrap metric `update_state()` with `add_update()`.
++    # Arguments
++        update_state_fn: function that accumulates metric statistics.
++    # Returns
++        Decorated function that wraps `update_state_fn()` with `add_update()`.
++    """
++    def decorated(metric_obj, *args, **kwargs):
++        """Decorated function with `add_update()`."""
++
++        update_op = update_state_fn(*args, **kwargs)
++        metric_obj.add_update(update_op)
++        return update_op
++
++    return decorated
++
++def result_wrapper(result_fn):
++    """Decorator to wrap metric `result()` with identity op.
++    Wrapping result in identity so that control dependency between
++    update_op from `update_state` and result works in case result returns
++    a tensor.
++    # Arguments
++        result_fn: function that computes the metric result.
++    # Returns
++        Decorated function that wraps `result()` with identity op.
++    """
++    def decorated(metric_obj, *args, **kwargs):
++        result_t = K.identity(result_fn(*args, **kwargs))
++        metric_obj._call_result = result_t
++        result_t._is_metric = True
++        return result_t
++    return decorated
++
++
++def to_list(x):
++    if isinstance(x, list):
++        return x
++    return [x]
++
++
++def assert_thresholds_range(thresholds):
++    if thresholds is not None:
++        invalid_thresholds = [t for t in thresholds if t is None or t < 0 or t > 1]
++    if invalid_thresholds:
++        raise ValueError(
++            'Threshold values must be in [0, 1]. Invalid values: {}'.format(
++            invalid_thresholds))
++
++
++def parse_init_thresholds(thresholds, default_threshold=0.5):
++    if thresholds is not None:
++        assert_thresholds_range(to_list(thresholds))
++    thresholds = to_list(default_threshold if thresholds is None else thresholds)
++    return thresholds
++
++class ConfusionMatrix(Enum):
++    TRUE_POSITIVES = 'tp'
++    FALSE_POSITIVES = 'fp'
++    TRUE_NEGATIVES = 'tn'
++    FALSE_NEGATIVES = 'fn'
++
++class AUCCurve(Enum):
++    """Type of AUC Curve (ROC or PR)."""
++    ROC = 'ROC'
++    PR = 'PR'
++
++    @staticmethod
++    def from_str(key):
++        if key in ('pr', 'PR'):
++            return AUCCurve.PR
++        elif key in ('roc', 'ROC'):
++            return AUCCurve.ROC
++        else:
++            raise ValueError('Invalid AUC curve value "%s".' % key)
++
++
++class AUCSummationMethod(Enum):
++    """Type of AUC summation method.
++
++    https://en.wikipedia.org/wiki/Riemann_sum)
++
++    Contains the following values:
++    * 'interpolation': Applies mid-point summation scheme for `ROC` curve. For
++    `PR` curve, interpolates (true/false) positives but not the ratio that is
++    precision (see Davis & Goadrich 2006 for details).
++    * 'minoring': Applies left summation for increasing intervals and right
++    summation for decreasing intervals.
++    * 'majoring': Applies right summation for increasing intervals and left
++    summation for decreasing intervals.
++    """
++    INTERPOLATION = 'interpolation'
++    MAJORING = 'majoring'
++    MINORING = 'minoring'
++
++    @staticmethod
++    def from_str(key):
++        if key in ('interpolation', 'Interpolation'):
++            return AUCSummationMethod.INTERPOLATION
++        elif key in ('majoring', 'Majoring'):
++            return AUCSummationMethod.MAJORING
++        elif key in ('minoring', 'Minoring'):
++            return AUCSummationMethod.MINORING
++        else:
++            raise ValueError('Invalid AUC summation method value "%s".' % key)
++
++def weighted_assign_add(label, pred, weights, var):
++    # Logical and
++    label = K.expand_dims(label, 0)
++    pred = K.expand_dims(pred, 0)
++    are_different = K.concatenate([label, pred], axis=0)
++    label_and_pred = K.all(are_different, axis=0)
++    label_and_pred = K.cast(label_and_pred, dtype=K.floatx())
++    if weights is not None:
++        label_and_pred *= weights
++    return var.assign_add(K.sum(label_and_pred, 1))
++
++def update_confusion_matrix_variables(variables_to_update,
++                                      y_true,
++                                      y_pred,
++                                      thresholds,
++                                      top_k=None,
++                                      class_id=None,
++                                      sample_weight=None):
++    """Returns op to update the given confusion matrix variables.
++    For every pair of values in y_true and y_pred:
++    true_positive: y_true == True and y_pred > thresholds
++    false_negatives: y_true == True and y_pred <= thresholds
++    true_negatives: y_true == False and y_pred <= thresholds
++    false_positive: y_true == False and y_pred > thresholds
++    The results will be weighted and added together. When multiple thresholds are
++    provided, we will repeat the same for every threshold.
++    For estimation of these metrics over a stream of data, the function creates an
++    `update_op` operation that updates the given variables.
++    If `sample_weight` is `None`, weights default to 1.
++    Use weights of 0 to mask values.
++    # Arguments
++    variables_to_update: Dictionary with 'tp', 'fn', 'tn', 'fp' as valid keys
++      and corresponding variables to update as values.
++    y_true: A `Tensor` whose shape matches `y_pred`. Will be cast to `bool`.
++    y_pred: A floating point `Tensor` of arbitrary shape and whose values are in
++      the range `[0, 1]`.
++    thresholds: A float value or a python list or tuple of float thresholds in
++      `[0, 1]`, or NEG_INF (used when top_k is set).
++    top_k: Optional int, indicates that the positive labels should be limited to
++      the top k predictions.
++    class_id: Optional int, limits the prediction and labels to the class
++      specified by this argument.
++    sample_weight: Optional `Tensor` whose rank is either 0, or the same rank as
++      `y_true`, and must be broadcastable to `y_true` (i.e., all dimensions must
++      be either `1`, or the same as the corresponding `y_true` dimension).
++    # Returns
++        Update ops.
++    # Raises
++        ValueError: If `y_pred` and `y_true` have mismatched shapes, or if
++            `sample_weight` is not `None` and its shape doesn't match `y_pred`, or if
++            `variables_to_update` contains invalid keys.
++    """
++    if variables_to_update is None:
++        return
++    y_true = K.cast(y_true, dtype=K.floatx())
++    y_pred = K.cast(y_pred, dtype=K.floatx())
++    if sample_weight is not None:
++        sample_weight = K.cast(sample_weight, dtype=K.floatx())
++
++    if not any(key
++               for key in variables_to_update
++               if key in list(ConfusionMatrix)):
++        raise ValueError(
++            'Please provide at least one valid confusion matrix '
++            'variable to update. Valid variable key options are: "{}". '
++            'Received: "{}"'.format(
++                list(ConfusionMatrix), variables_to_update.keys()))
++
++    invalid_keys = [
++        key for key in variables_to_update if key not in list(ConfusionMatrix)
++    ]
++    if invalid_keys:
++        raise ValueError(
++            'Invalid keys: {}. Valid variable key options are: "{}"'.format(
++                invalid_keys, list(ConfusionMatrix)))
++
++    if sample_weight is None:
++        y_pred, y_true = losses_utils.squeeze_or_expand_dimensions(
++            y_pred, y_true=y_true)
++    else:
++        y_pred, y_true, sample_weight = (
++            losses_utils.squeeze_or_expand_dimensions(
++                y_pred, y_true=y_true, sample_weight=sample_weight))
++
++    if top_k is not None:
++        y_pred = _filter_top_k(y_pred, top_k)
++    if class_id is not None:
++        y_true = y_true[..., class_id]
++        y_pred = y_pred[..., class_id]
++
++    thresholds = to_list(thresholds)
++    num_thresholds = len(thresholds)
++    num_predictions = K.size(y_pred)
++
++    # Reshape predictions and labels.
++    predictions_2d = K.reshape(y_pred, [1, -1])
++    labels_2d = K.reshape(
++        K.cast(y_true, dtype='bool'), [1, -1])
++
++    # Tile the thresholds for every prediction.
++    thresh_tiled = K.tile(
++        K.expand_dims(K.constant(thresholds), 1),
++        K.stack([1, num_predictions]))
++
++    # Tile the predictions for every threshold.
++    preds_tiled = K.tile(predictions_2d, [num_thresholds, 1])
++
++    # Compare predictions and threshold.
++    pred_is_pos = K.greater(preds_tiled, thresh_tiled)
++    pred_is_neg = K.greater(thresh_tiled, preds_tiled)
++
++    # Tile labels by number of thresholds
++    label_is_pos = K.tile(labels_2d, [num_thresholds, 1])
++
++    if sample_weight is not None:
++        weights = losses_utils.broadcast_weights(
++            y_pred, K.cast(sample_weight, dtype=K.floatx()))
++        weights_tiled = K.tile(
++            K.reshape(weights, [1, -1]), [num_thresholds, 1])
++    else:
++        weights_tiled = None
++
++    update_ops = []
++    loop_vars = {
++        ConfusionMatrix.TRUE_POSITIVES: (label_is_pos, pred_is_pos),
++    }
++    update_tn = ConfusionMatrix.TRUE_NEGATIVES in variables_to_update
++    update_fp = ConfusionMatrix.FALSE_POSITIVES in variables_to_update
++    update_fn = ConfusionMatrix.FALSE_NEGATIVES in variables_to_update
++
++    if update_fn or update_tn:
++        loop_vars[ConfusionMatrix.FALSE_NEGATIVES] = (label_is_pos, pred_is_neg)
++
++    if update_fp or update_tn:
++        label_is_neg = K.equal(
++            label_is_pos, K.zeros_like(label_is_pos, dtype=label_is_pos.dtype))
++        loop_vars[ConfusionMatrix.FALSE_POSITIVES] = (label_is_neg, pred_is_pos)
++    if update_tn:
++        loop_vars[ConfusionMatrix.TRUE_NEGATIVES] = (label_is_neg, pred_is_neg)
++
++    for matrix_cond, (label, pred) in loop_vars.items():
++        if matrix_cond in variables_to_update:
++            update_ops.append(
++                weighted_assign_add(label, pred, weights_tiled,
++                                    variables_to_update[matrix_cond]))
++    return update_ops
++
+-- 
+2.26.2
+
-- 
cgit v1.2.3


From 91f441b91dd00372263a3956f7682df56151f948 Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Sun, 26 Apr 2020 07:05:24 -0500
Subject: gn: Add python-scanpy-git: 1.4.6-1.590d423

---
 gn/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

(limited to 'gn')

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 02ac1e8..056bc3f 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -1266,3 +1266,43 @@ COVID-19 Virtual Biohackathon's Public Sequence Resource project.  You can use
 it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely
 available to other researchers.")
       (license license:asl2.0))))
+
+(define-public python-scanpy-git
+  (let ((commit "590d42309f9ed6550d7b887039990edfc1ac7648") ; April 22, 2020
+        (revision "1"))
+    (package
+      (inherit python-scanpy)
+      (name "python-scanpy-git")
+      (version (git-version "1.4.6" revision commit))
+      (source
+        (origin
+          (method git-fetch)
+          (uri (git-reference
+                 (url "https://github.com/theislab/scanpy")
+                 (commit commit)))
+          (file-name (git-file-name "python-scanpy" version))
+          (sha256
+           (base32 "0z3pk9vh4b7fqq7fs262i6z0pm1dnn6bf49a4r7r73k6gjj6namd"))))
+      (arguments
+       (substitute-keyword-arguments (package-arguments python-scanpy)
+         ((#:phases phases)
+          `(modify-phases ,phases
+             (add-before 'build 'fix-build
+               (lambda* (#:key inputs outputs #:allow-other-keys)
+                 (let ((out (assoc-ref outputs "out"))
+                       (pyv (python-version (assoc-ref inputs "python"))))
+                   (substitute* "setup.py"
+                     (("use_scm_version=True") "use_scm_version=False"))
+                   (substitute* "scanpy/__init__.py"
+                     (("__version__.*")
+                      (string-append "__version__ = '" ,version "'\n")))
+                   (mkdir-p
+                     (string-append out "/lib/python" pyv "/site-packages"))
+                   (setenv "PYTHONPATH"
+                           (string-append out
+                                          "/lib/python" pyv "/site-packages/:"
+                                          (getenv "PYTHONPATH"))))
+                 ;; These tests fail on this git revision
+                 (delete-file "scanpy/tests/test_neighbors_key_added.py")
+                 (delete-file "scanpy/tests/test_pca.py")
+                 #t)))))))))
-- 
cgit v1.2.3


From 3b5182bdd5d9a24cbc15c47df6acbfdbc1c80d3a Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Mon, 27 Apr 2020 04:57:49 -0500
Subject: gn: Add hrdp-project

---
 gn/packages/ratspub.scm | 93 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 93 insertions(+)

(limited to 'gn')

diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm
index 9dd9745..b664799 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -9,6 +9,7 @@
   #:use-module (gnu packages bioinformatics)
   #:use-module (gn packages javascript)
   #:use-module (gnu packages machine-learning)
+  #:use-module (gnu packages python)
   #:use-module (gnu packages python-crypto)
   #:use-module (gnu packages python-web)
   #:use-module (gnu packages python-xyz)
@@ -155,3 +156,95 @@ question.")
          ((#:phases phases)
           `(modify-phases ,phases
              (delete 'check))))))))
+
+(define-public hrdp-project
+  (package
+    (name "hrdp-project")
+    (version "0.1")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/noderboarder/hrdp-project")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1ag7jm43p35yh0cqcn53wg4iw7sgfypw10mxq5klxvhgj3r6cf7i"))))
+    (build-system python-build-system)
+    (arguments
+     `(#:tests? #f  ; no test suite
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'build)
+         (add-after 'unpack 'patch-sources
+           (lambda _
+             (substitute* "./app/templates/layout.html"
+               (("https://.*.bootstrapcdn.com/bootstrap/4.*/css/bootstrap.min.css.*")
+                "/static/bootstrap.min.css\">\n")
+               (("https://.*.bootstrapcdn.com/bootstrap/4.*/js/bootstrap.min.js.*")
+                "/static/bootstrap.min.js\"></script>\n")
+               (("https://code.jquery.com/jquery-3.*.slim.min.js.*")
+                "/static/jquery.slim.min.js\"></script>\n")
+               ;(("https://cdn.jsdelivr.net/npm/popper.js@1.16.0/dist/umd/popper.min.js.*")
+               ; "/static/popper.min.js\"></script>\n")
+               )
+             #t))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out (assoc-ref outputs "out"))
+                   (python (assoc-ref inputs "python")))
+               (delete-file "main.py")
+               (with-output-to-file "main.py"
+                 (lambda ()
+                   (format #t "#!~a/bin/python
+from app import create_app
+
+app = create_app()
+
+if __name__ == '__main__':
+    app.run(debug=True, port=4222)~%"
+                   python)))
+               (chmod "main.py" #o555)
+               (copy-recursively "." out))
+             #t))
+         (add-after 'install 'install-javascript
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out       (assoc-ref outputs "out"))
+                   (bootstrap (assoc-ref inputs "bootstrap"))
+                   (jquery    (assoc-ref inputs "jquery"))
+                   ;(js-popper (assoc-ref inputs "js-popper"))
+                   )
+               (symlink (string-append bootstrap
+                                       "/share/web/bootstrap/css/bootstrap.min.css")
+                        (string-append out "/app/static/bootstrap.min.css"))
+               (symlink (string-append bootstrap
+                                       "/share/web/bootstrap/js/bootstrap.min.js")
+                        (string-append out "/app/static/bootstrap.min.js"))
+               (symlink (string-append jquery
+                                       "/share/web/jquery/jquery.slim.min.js")
+                        (string-append out "/app/static/jquery.slim.min.js"))
+               ;(symlink (string-append js-popper
+               ;                        "/share/web/popper/popper.min.js")
+               ;         (string-append out "/static/popper.min.js"))
+               )
+             #t))
+         (add-after 'install 'wrap-executable
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((out  (assoc-ref outputs "out"))
+                   (path (getenv "PYTHONPATH")))
+               (wrap-program (string-append out "/main.py")
+                `("PYTHONPATH" ":" prefix (,path))))
+             #t)))))
+    (inputs
+     `(("python" ,python)
+       ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)))
+    (native-inputs
+     `(("bootstrap" ,web-bootstrap)
+       ("jquery" ,web-jquery)
+       ;("js-popper" ,js-popper)    ; empty output
+       ))
+    (home-page "https://github.com/noderboarder/hrdp-project")
+    (synopsis "")
+    (description "")
+    (license license:expat)))
-- 
cgit v1.2.3


From 5390e28c3308d0f9ce7ee2b96c9c4f31e3a7861b Mon Sep 17 00:00:00 2001
From: Efraim Flashner
Date: Tue, 28 Apr 2020 06:21:57 -0500
Subject: gn: graphviz-2.26: Build without bindings.

[configure-flags]: Drop 'enable-python24'. Add 'enable-swig=no'
[inputs]: Remove python2.4, swig.
---
 gn/packages/graphviz.scm | 9 +++------
 1 file changed, 3 insertions(+), 6 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/graphviz.scm b/gn/packages/graphviz.scm
index 81e745c..33b15a1 100644
--- a/gn/packages/graphviz.scm
+++ b/gn/packages/graphviz.scm
@@ -3,7 +3,6 @@
   #:use-module (guix packages)
   #:use-module (guix download)
   #:use-module (guix utils)
-  #:use-module (gn packages python24)
   #:use-module (gnu packages gl)
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages gtk)
@@ -28,18 +27,16 @@
           "18bzyg17ni0lpcd2g5dhan8fjv3vzkjym38jq8vm42did5p9j47l"))))
     ;; TODO: unbundle libraries?
     (arguments
-     `(#:configure-flags '("--enable-python24=yes")
+     `(#:configure-flags '("--enable-swig=no")
        ,@(substitute-keyword-arguments (package-arguments graphviz)
            ((#:phases phases)
             `(modify-phases ,phases
                (delete 'move-docs) ; one output
                (delete 'move-guile-bindings))))))
     (inputs
-      ;; TODO: Add(?) perl, guile@1.8, gtk@2, lua5.1, tcl8.[3-6], rsvg
+      ;; TODO(?): Add perl, guile@1.8, gtk@2, lua5.1, tcl8.[3-6], rsvg, python-2.4
      `(("gdk-pixbuf" ,gdk-pixbuf)
-       ;("ghostscript" ,ghostscript)
        ("freeglut" ,freeglut)
-       ("python2.4" ,python-2.4)
        ,@(fold alist-delete (package-inputs graphviz)
-               '("libjpeg" "guile"))))
+               '("libjpeg" "guile" "swig"))))
     (license license:cpl1.0)))
-- 
cgit v1.2.3