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

4 files changed, 157 insertions, 66 deletions

diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 90735fe..5e9b4b7 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -57,7 +57,7 @@
   #:use-module (gnu packages web)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages bootstrap)
-  #:use-module (gn packages ldc)
+  ; #:use-module (gn packages ldc)
   #:use-module (gn packages ldc)
   #:use-module (gn packages shell)
   #:use-module (srfi srfi-1))
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 9d8fd91..8181e3e 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -28,7 +28,7 @@
   #:use-module (gnu packages graphviz)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
-  #:use-module (gnu packages ldc)
+  ; #:use-module (gnu packages ldc)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages ncurses)
@@ -272,7 +272,11 @@ location of a putative QTL.")
               ("python2-unittest2" ,python2-unittest2)
               ("python2-xlsxwriter" ,python2-xlsxwriter)
               ("python2-qtlreaper" ,python2-qtlreaper)
-              ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher)
+	            ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher)
+	            ("javascript-cytoscape" ,javascript-cytoscape)
+	            ("javascript-panzoom" ,javascript-cytoscape-panzoom)
+	            ("javascript-qtip" ,javascript-cytoscape-qtip)
+
               ))
     (build-system python-build-system)
     (arguments
@@ -437,7 +441,9 @@ location of a putative QTL.")
 	("python-parameterized" ,python-parameterized) ;; used for the tests
 	("genenetwork2-files-small" ,genenetwork2-files-small)
 	("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher)
-
+	("javascript-cytoscape" ,javascript-cytoscape)
+	("javascript-panzoom" ,javascript-cytoscape-panzoom)
+	("javascript-qtip" ,javascript-cytoscape-qtip)
 
 	;; With Python3 support
 	("python-wrapper" ,python-wrapper)
diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm
index 7fc82af..a964405 100644
--- a/gn/packages/javascript.scm
+++ b/gn/packages/javascript.scm
@@ -1,5 +1,7 @@
 (define-module (gn packages javascript)
   #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages compression)
   #:use-module (gnu packages)
   #:use-module (guix packages)
   #:use-module (guix download)
@@ -9,38 +11,155 @@
   #:use-module (guix build-system trivial)
   #:use-module (srfi srfi-1))
 
+;; see color-make package for great example - also install-file and invoke
+
 (define-public javascript-twitter-post-fetcher
   (let ((commit "27440ffebd4c1ba7abc9aec92a581155715f2e4e"))
+    (package
+     (name "javascript-twitter-post-fetcher")
+     (version (string-append "17.0.3" "-" (string-take commit 7)))
+     (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/jasonmayes/Twitter-Post-Fetcher.git")
+                    (commit commit)))
+              (file-name (string-append name "-" commit))
+              (sha256
+               (base32
+                "159z8izf510086d8sa79k4mml6sw1gycb1r1r9ri1kyw2k9knmqa"))))
+     (build-system trivial-build-system)
+     (native-inputs `(("source" ,source)))
+     (arguments
+      `(#:modules ((guix build utils))
+        #:builder
+        (let* ((out (assoc-ref %outputs "out"))
+               (name "Twitter-Post-Fetcher")
+               (targetdir (string-append out "/share/genenetwork2/javascript/" name))
+               )
+          (begin
+            (use-modules (guix build utils))
+            (let ((source (assoc-ref %build-inputs "source"))
+                  )
+              (and
+                                        ; (mkdir-p targetdir)
+               (copy-recursively source targetdir)
+               ))))))
+     (home-page "http://jasonmayes.com/projects/twitterApi/")
+     (synopsis "Twitter post fetching")
+     (description "Twitter post fetching.")
+     (license license:expat))))
+
+(define-public javascript-cytoscape
   (package
-    (name "javascript-twitter-post-fetcher")
-    (version (string-append "17.0.3" "-" (string-take commit 7)))
-    (source (origin
-             (method git-fetch)
-             (uri (git-reference
-                   (url "https://github.com/jasonmayes/Twitter-Post-Fetcher.git")
-                   (commit commit)))
-             (file-name (string-append name "-" commit))
-             (sha256
-              (base32
-               "159z8izf510086d8sa79k4mml6sw1gycb1r1r9ri1kyw2k9knmqa"))))
+    (name "javascript-cytoscape")
+    (version "2.7.8") ; ancient version
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "https://github.com/cytoscape/cytoscape.js/archive/v" version ".tar.gz"))
+       (file-name (string-append name "-" version ".tar.gz"))
+       (sha256
+        (base32 "08ks2nd7ccmdmahn151i180pvhn4vdzgpw99g4g4f2baz9pkz4w3"))))
     (build-system trivial-build-system)
-    (native-inputs `(("source" ,source)))
+    (native-inputs `(("gzip" ,gzip)
+                     ("tar" ,tar)
+                     ("source" ,source)))
     (arguments
      `(#:modules ((guix build utils))
        #:builder
-       (let* ((out (assoc-ref %outputs "out"))
-              (name "Twitter-Post-Fetcher")
-              (targetdir (string-append out "/share/genenetwork2/javascript/" name))
-              )
-           (begin
-             (use-modules (guix build utils))
-             (let ((source (assoc-ref %build-inputs "source"))
-                   )
-               (and
-                    ; (mkdir-p targetdir)
-                    (copy-recursively source targetdir)
-                    ))))))
-    (home-page "http://jasonmayes.com/projects/twitterApi/")
-    (synopsis "Twitter post fetching")
-    (description "Twitter post fetching.")
-    (license license:expat))))
+       (begin
+         (use-modules (guix build utils))
+         (let* ((out (assoc-ref %outputs "out"))
+                (tarcmd (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))
+                (targetdir (string-append out "/share/genenetwork2/javascript/cytoscape"))
+                (source (assoc-ref %build-inputs "source")))
+           (setenv "PATH" (string-append
+                           (assoc-ref %build-inputs "tar") "/bin" ":"
+                           (assoc-ref %build-inputs "gzip") "/bin"))
+           (invoke "tar" "xvf" (assoc-ref %build-inputs "source") "--strip-components=1")
+           (mkdir-p targetdir)
+           (copy-recursively "dist" targetdir)
+           ))))
+
+    (home-page "https://github.com/cytoscape/cytoscape.js")
+    (synopsis "Cytoscape.js")
+    (description "Cytoscape.")
+    (license license:expat)))
+
+(define-public javascript-cytoscape-panzoom
+  (package
+   ;; (inherit javascript-cytoscape)
+   (name "javascript-cytoscape-panzoom")
+   (version "2.5.2") ; ancient version
+   (source
+    (origin
+     (method url-fetch)
+     (uri (string-append "https://github.com/cytoscape/cytoscape.js-panzoom/archive/" version ".tar.gz"))
+     (file-name (string-append name "-" version ".tar.gz"))
+     (sha256
+      (base32 "154xzi693gbv89y221gkpi03k84lccmr55v5z43mn1i1s1fdhm2b"))))
+   (inputs `(("javascript-cytoscape" ,javascript-cytoscape)))
+   (build-system trivial-build-system)
+   (native-inputs `(("gzip" ,gzip)
+                    ("tar" ,tar)
+                    ("source" ,source)))
+   (arguments
+    `(#:modules ((guix build utils))
+      #:builder
+      (begin
+        (use-modules (guix build utils))
+        (let* ((out (assoc-ref %outputs "out"))
+               (tarcmd (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))
+               (targetdir (string-append out "/share/genenetwork2/javascript/cytoscape-panzoom"))
+               (source (assoc-ref %build-inputs "source")))
+          (setenv "PATH" (string-append
+                          (assoc-ref %build-inputs "tar") "/bin" ":"
+                          (assoc-ref %build-inputs "gzip") "/bin"))
+          (invoke "tar" "xvf" (assoc-ref %build-inputs "source") "--strip-components=1")
+          (mkdir-p targetdir)
+          (install-file "cytoscape-panzoom.js" targetdir)
+          (install-file "cytoscape.js-panzoom.css" targetdir)
+          ))))
+    (home-page "https://github.com/cytoscape/cytoscape.js")
+    (synopsis "Cytoscape.js")
+    (description "Cytoscape.")
+    (license license:expat)))
+
+;; https://github.com/cytoscape/cytoscape.js-qtip/archive/2.7.1.tar.gz
+(define-public javascript-cytoscape-qtip
+  (package
+   ;; (inherit javascript-cytoscape)
+   (name "javascript-cytoscape-qtip")
+   (version "2.7.1") ; ancient version
+   (source
+    (origin
+     (method url-fetch)
+     (uri (string-append "https://github.com/cytoscape/cytoscape.js-qtip/archive/" version ".tar.gz"))
+     (file-name (string-append name "-" version ".tar.gz"))
+     (sha256
+      (base32 "0f2qhxi9qx5r3rcmxqgdqnwd9apnjlb4s4hckwhaqgsp6rf8lzlb"))))
+   (inputs `(("javascript-cytoscape" ,javascript-cytoscape)))
+   (build-system trivial-build-system)
+   (native-inputs `(("gzip" ,gzip)
+                    ("tar" ,tar)
+                    ("source" ,source)))
+   (arguments
+    `(#:modules ((guix build utils))
+      #:builder
+      (begin
+        (use-modules (guix build utils))
+        (let* ((out (assoc-ref %outputs "out"))
+               (tarcmd (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))
+               (targetdir (string-append out "/share/genenetwork2/javascript/cytoscape-qtip"))
+               (source (assoc-ref %build-inputs "source")))
+          (setenv "PATH" (string-append
+                          (assoc-ref %build-inputs "tar") "/bin" ":"
+                          (assoc-ref %build-inputs "gzip") "/bin"))
+          (invoke "tar" "xvf" (assoc-ref %build-inputs "source") "--strip-components=1")
+          (mkdir-p targetdir)
+          (install-file "cytoscape-qtip.js" targetdir)
+          ))))
+    (home-page "https://github.com/cytoscape/cytoscape.js")
+    (synopsis "Cytoscape.js")
+    (description "Cytoscape.")
+    (license license:expat)))
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index ff8bf57..f254ce3 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -64,40 +64,6 @@
     "Variant Call Format (VCF) parser for Python")
    (license #f)))
 
-
-(define-public python-elasticsearch
-  (package
-    (name "python-elasticsearch")
-    (version "6.1.1")
-    (source
-      (origin
-        (method url-fetch)
-        (uri (pypi-uri "elasticsearch" version))
-        (sha256
-         (base32
-          "1kjxl45yvvgfb5fmamx0kfsfg9pzphiqrwbkns3s28r1w7ya74cd"))))
-    (build-system python-build-system)
-    (native-inputs
-     `(("python-mock" ,python-mock)
-       ("python-nosexcover" ,python-nosexcover)
-       ("python-pyaml" ,python-pyaml)
-       ("python-requests" ,python-requests)))
-    (propagated-inputs
-     `(("urllib3" ,python-urllib3)))
-    (arguments
-     ;; tests require the test_elasticsearch module but it is not distributed.
-     `(#:tests? #f))
-    (home-page "https://github.com/elastic/elasticsearch-py")
-    (synopsis "Low-level client for Elasticsearch")
-    (description "Official low-level client for Elasticsearch.  Its goal is to
-provide common ground for all Elasticsearch-related code in Python; because of
-this it tries to be opinion-free and very extendable.")
-    (license license:expat)))
-
-(define-public python2-elasticsearch
-  (package-with-python2 python-elasticsearch))
-
-
 (define-public python2-rpy2
   (package
     (name "python2-rpy2")