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-rw-r--r--gn/packages/bioinformatics.scm30
-rw-r--r--gn/packages/bnw.scm140
-rw-r--r--gn/packages/maths.scm1
-rw-r--r--gn/packages/ratspub.scm5
-rw-r--r--gn/services/archive-pubmed.service13
-rw-r--r--gn/services/archive-pubmed.timer9
-rw-r--r--gn/services/bnw-container.scm4
7 files changed, 131 insertions, 71 deletions
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)
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")))
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
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
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
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"