Merge branch 'master' of gitlab.com:genenetwork/guix-bioinformatics

5 files changed, 121 insertions, 46 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 4f133f8..4b8e16b 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -857,6 +857,67 @@ grants require a calculation of the applications power to detect the effect of
 interest, and this app can provide values and figures for applicants to use.")
         (license license:gpl3))))
 
+(define-public singlecellrshiny
+  (let ((commit "8061dcb477ba355de77d3e4fd3a15cf3267b56af")
+        (revision "1"))
+    (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")
+              (commit commit)))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "1pd8a9jx6ijjggsifvq66madx31h29rah5pmz4kdzfzb4fskpqz1"))))
+     (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)
+            (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") "")
+              )
+            (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=4208)~%\n"
+                Rbin targetdir)))
+            (chmod app #o555)
+            #t))))
+     (native-inputs `(("source" ,source)))
+     (inputs
+      `(("r-min" ,r-minimal)))
+     (propagated-inputs
+      `(("r" ,r)
+        ("r-dt" ,r-dt)
+        ("r-seurat" ,r-seurat)
+        ("r-shiny" ,r-shiny)))
+     (home-page "http://rn6err.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))))
+
 (define-public seqwish
   (package
     (name "seqwish")
diff --git a/gn/packages/bnw.scm b/gn/packages/bnw.scm
index bdb6ac5..f7e95e3 100644
--- a/gn/packages/bnw.scm
+++ b/gn/packages/bnw.scm
@@ -14,7 +14,7 @@
 
 (define-public bnw
   (let ((commit "eb6b002b924694808384f1a8d7c6d1121806ae04")
-        (revision "3"))
+        (revision "4"))
     (package
       (name "bnw")
       (version (git-version "1.22" revision commit)) ; June 28, 2019
@@ -41,6 +41,9 @@
                  (("http://bnw.genenetwork.org/BNW_1.22") "http://bnw-test.genenetwork.org"))
                (substitute* "sourcecodes/header_batchsearch.inc"
                  (("my_style.css") "my_new_style.css"))
+               (substitute* (find-files "." "\\.php")
+                 (("HTTP_POST_VARS") "_POST")
+                 (("HTTP_POST_FILES") "_FILES"))
                #t))
            (add-after 'patch-source-shebangs 'patch-more-shebangs
              (lambda* (#:key inputs #:allow-other-keys)
@@ -70,48 +73,51 @@
                    (find-files "." ".*"))
                  (substitute* '("sourcecodes/examplefilecopy.sh"
                                 "sourcecodes/filecopy.sh")
-                   (("rm") (which "rm"))
-                   (("cp") (which "cp")))
+                   (("^rm") (which "rm"))
+                   (("\\ cp") (string-append " " (which "cp"))))
+                 (substitute* (find-files "sourcecodes" "(^run|py$)")
+                   (("/home/jziebart/python/Python-2.7.15/python") (which "python2")))
                  (substitute*
                    (append (find-files "sourcecodes" ".php")
                            (find-files "sourcecodes/run_scripts" ".*"))
                    (("/usr/bin/dot") (string-append graphviz "/bin/dot")))
-                 (substitute* "sourcecodes/build.sh"
+                 (substitute* '("sourcecodes/build.sh"
+                                "downloads/BNW/src/build.sh")
                    (("./localscore/libRmath.so") (string-append rmath "/lib/libRmath.so")))
-                 (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"))))
+                 ;(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))
            (replace 'install
              (lambda* (#:key outputs #:allow-other-keys)
                (let ((out (assoc-ref outputs "out")))
-                 (delete-file "sourcecodes/localscore/libRmath.so")
                  (copy-recursively "." out))
                #t))
            (add-after 'install 'make-files-executable
@@ -120,28 +126,30 @@
                  (for-each
                    (lambda (file)
                      (chmod file #o555))
-                   (find-files out "\\.sh$"))
+                   (append (find-files out "\\.(sh|py)$")
+                           (find-files (string-append out "/sourcecodes/run_scripts" ".*"))
+                           ))
                  #t)))
            (replace 'build
              (lambda _
                (with-directory-excursion "sourcecodes"
                  (substitute* "build.sh"
                    (("./localscore") "localscore"))
-                 (chmod "k-best/src/buildk_poster.sh" #o755)
+                 (chmod "k-best/src/buildk_poster.sh" #o555)
                  (invoke "sh" "build.sh")
                  ;; from info_files/plotly_notes.txt
                  ;(with-directory-excursion "data"
                  ;  (setenv "HOME" "/tmp")
                  ;  (invoke "python" "../cv_plotly.py" "LvQ")
                  ;  (invoke "sh" "../plotly_loo.sh"))
-                 ;(invoke "./run_loo" "LvQ Weight")
+                 ;(invoke "./run_scripts/run_loo" "LvQ Weight")
                  ))))))
       (inputs
        `(("graphviz" ,graphviz-2.26)
          ("octave" ,octave-3.4.3)
          ("python" ,python-2)
          ("plotly" ,python2-plotly-3.2.1)
-         ("rmath" ,rmath-standalone) ; Should this be r-minimal? Which version?
+         ("rmath" ,rmath-standalone)
          ("jquery" ,web-jquery)
          ("awesome" ,web-font-awesome)
          ("cytoscape" ,javascript-cytoscape)
diff --git a/gn/services/bnw-container.scm b/gn/services/bnw-container.scm
index cd8562f..13a9317 100644
--- a/gn/services/bnw-container.scm
+++ b/gn/services/bnw-container.scm
@@ -1,6 +1,7 @@
 (define-module (gn services bnw-container))
 
-(use-modules (gnu))
+(use-modules (gnu)
+             (gn packages bnw))
 (use-service-modules base networking web)
 
 (operating-system
@@ -22,9 +23,14 @@
                              (server-blocks
                                (list
                                  (nginx-server-configuration
-                                   (root "/srv/http/bnw")
+                                   (server-name '("Bayesian Network"))
+                                   (listen '("8888"))
+                                   (root bnw)
                                    (locations
-                                     (list (nginx-php-location)))
-                                   (listen '("8880"))
-                                   (ssl-certificate #f)
-                                   (ssl-certificate-key #f)))))))))
+                                     (list
+                                       (nginx-php-location)
+                                       (nginx-location-configuration
+                                         (uri "/sourcecodes/data/")
+                                         (body (list "alias /tmp/bnw/;")))
+                                       ))
+                                   ))))))))
diff --git a/gn/services/gitea-dump.service b/gn/services/gitea-dump.service
index b9b310d..c177334 100644
--- a/gn/services/gitea-dump.service
+++ b/gn/services/gitea-dump.service
@@ -4,7 +4,7 @@ Wants=gitea.service
 
 [Service]
 Type=oneshot
-Environment="GITEA_COMMAND=$(GUIX_PACKAGE_PATH=/home/efraimf/workspace/guix-bioinformatics /var/guix/profiles/per-user/efraimf/current-guix/bin/guix build gitea)/bin/gitea"
+Environment="GITEA_COMMAND=/usr/local/guix-profiles/gitea/bin/gitea"
 ExecStart=/bin/su -l gitea -c 'GITEA_WORK_DIR=/var/lib/git/gitea HOME=/var/lib/git/gitea ${GITEA_COMMAND} dump'
 
 [Install]
diff --git a/gn/services/gitea-nocontainer.service b/gn/services/gitea-nocontainer.service
index b18e235..6784e51 100644
--- a/gn/services/gitea-nocontainer.service
+++ b/gn/services/gitea-nocontainer.service
@@ -3,7 +3,7 @@ Description=Gitea git server and web ui
 Wants=guix-daemon.service
 
 [Service]
-Environment="GITEA_COMMAND=$(GUIX_PACKAGE_PATH=/home/efraimf/workspace/guix-bioinformatics /var/guix/profiles/per-user/efraimf/current-guix/bin/guix build gitea)/bin/gitea"
+Environment="GITEA_COMMAND=/usr/local/guix-profiles/gitea/bin/gitea"
 ExecStart=/bin/su -l gitea -c 'GITEA_WORK_DIR=/var/lib/git/gitea HOME=/var/lib/git/gitea ${GITEA_COMMAND} --port 3300'
 
 [Install]