Merge branch 'master' of http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics

11 files changed, 891 insertions, 311 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 8897752..056bc3f 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -14,6 +14,8 @@
   #: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)
   #:use-module (gnu packages check)
@@ -22,6 +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)
@@ -31,9 +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
@@ -415,92 +422,7 @@ 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
-         ;   (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 '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.*") "")))
-                #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")))
-                  (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"))
-                  (copy-file xtract.linux (string-append bin "/xtract.Linux"))
-                  (copy-file rchive.linux (string-append bin "/rchive.Linux"))
-                  (chmod (string-append bin "/xtract.Linux") #o555)
-                  (chmod (string-append bin "/rchive.Linux") #o555))
-                #t))
-            (replace 'wrap-program
-              (lambda* (#:key outputs #:allow-other-keys)
-                ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
-                (let ((out (assoc-ref outputs "out"))
-                      (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")))
-                #t))))))
-    (inputs
-     `(("gzip" ,gzip)
-       ,@(package-inputs edirect)))
-    (native-inputs
-     `(
-       ;("go" ,go)
-       ("xtract.Linux"
-        ,(origin
-           (method url-fetch)
-           (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
-                               "/xtract.Linux")) ;; March 10, 2016
-           (sha256
-            (base32
-             "15yhhh8kfipk12rhzabap81ys8wgj0khn0mp8p7zwqhq028fwj0l"))))
-       ("rchive.Linux"
-        ,(origin
-           (method url-fetch)
-           (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/"
-                               "/rchive.Linux")) ;; November 14, 2017
-           (sha256
-            (base32
-             "0hl8zj1md9xbmaj0pv99rjyisw8w74rirw97xwqk47dz8v8ml338"))))))
-    (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"))))
+  (deprecated-package "edirect-gn" edirect))
 
 ;; TODO: Unbundle zlib, bamtools, tclap
 (define-public sniffles
@@ -856,19 +778,19 @@ 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 "3"))
     (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))
@@ -880,16 +802,20 @@ 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"))
+                 (800-H1    (assoc-ref %build-inputs "800-H1-H20-RNA-Seq.csv"))
                  (source    (assoc-ref %build-inputs "source")))
             (copy-recursively source targetdir)
+            (substitute* (string-append targetdir "/app.R")
+              ;; 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") "")
-              ;(("RobTop1001.csv") "")
-              )
+              (("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"))
             (mkdir-p (string-append out "/bin"))
             (call-with-output-file app
               (lambda (port)
@@ -901,20 +827,41 @@ runApp(launch.browser=0, port=4208)~%\n"
                 Rbin targetdir)))
             (chmod app #o555)
             #t))))
-     (native-inputs `(("source" ,source)))
      (inputs
-      `(("r-min" ,r-minimal)))
+      `(("r-min" ,r-minimal)
+        ("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"))))
+        ("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 "http://singlecell.opar.io/")
      (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 license:gpl3))))
+     (license license:agpl3))))
 
 (define-public seqwish
   (package
@@ -1193,3 +1140,169 @@ 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))))
+
+(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))))
+
+(define-public bh20-seq-resource
+  (let ((commit "bbca5ac9b2538e410efe3e09651f87e5573145de")
+        (revision "2"))
+    (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 "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
+       `(("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-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)))))))))
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/cran.scm b/gn/packages/cran.scm
new file mode 100644
index 0000000..d92f9f3
--- /dev/null
+++ b/gn/packages/cran.scm
@@ -0,0 +1,29 @@
+(define-module (gn 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)))
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/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)))
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/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)))
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))
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/python.scm b/gn/packages/python.scm
index 60558a2..7e4786f 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)
@@ -30,6 +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)
@@ -228,25 +230,6 @@ 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")
@@ -322,39 +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 "0.4.0")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "rdflib-jsonld" version))
-        (sha256
-          (base32
-            "0bdw2pbjmpy1l4p6slsjn54bqy6crk5hk4san84xxirgd9w78iql"))))
-    (build-system python-build-system)
-    (inputs
-      `(("python-setuptools" ,python-setuptools)))
-    (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")
-    (description
-      "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")
@@ -1094,3 +1044,142 @@ spreadsheets without the need for COM objects.")
     (synopsis "")
     (description "")
     (license license:bsd-4)))
+
+(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))
+
+(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"))))))
+
+(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/ratspub.scm b/gn/packages/ratspub.scm
index 29e1313..b664799 100644
--- a/gn/packages/ratspub.scm
+++ b/gn/packages/ratspub.scm
@@ -1,11 +1,16 @@
 (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)
   #:use-module (gnu packages admin)
-  #:use-module (gn packages bioinformatics)
+  #: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)
   #:use-module (gn packages web))
@@ -13,19 +18,27 @@
 (define-public ratspub
   (package
     (name "ratspub")
-    (version "0.1")
+    (version "0.3.1")
     (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
+                "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
+     `(#:tests? #f  ; no test suite
        #:phases
        (modify-phases %standard-phases
          (delete 'configure)
@@ -34,12 +47,24 @@
            (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))
@@ -51,31 +76,58 @@
          (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"))))
-                 `("PYTHONPATH" ":" prefix (,path))))
+                `("PATH" ":" prefix (,(dirname (which "edirect.pl"))
+                                      ,(dirname (which "dirname"))
+                                      ,(dirname (which "grep"))
+                                      ,(dirname (which "sed"))))
+                `("PYTHONPATH" ":" prefix (,path))))
              #t)))))
     (inputs
-     `(("edirect" ,edirect-gn)
+     `(("edirect" ,edirect)
        ("inetutils" ,inetutils)
-       ("python-flask" ,python-flask)
-       ("python-nltk" ,python-nltk)))
+       ("python-bcrypt" ,python-bcrypt)
+       ("python-flask-sqlalchemy" ,python-flask-sqlalchemy)
+       ("python-keras" ,python-keras-for-ratspub)
+       ("python-nltk" ,python-nltk)
+       ("tensorflow" ,tensorflow)))
     (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)    ; empty output
+       ))
     (home-page "http://rats.pub/")
     (synopsis "Relationship with Addiction Through Searches of PubMed")
     (description
@@ -86,4 +138,113 @@ 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)))
+
+;; 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)
+          `(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)))