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authorMuriithi Frederick Muriuki2018-04-08 11:35:00 +0300
committerMuriithi Frederick Muriuki2018-04-08 11:35:00 +0300
commitb7853e6340adc3bc10cc48931db7c8f2ebe8c2d5 (patch)
tree79f98d79f7c4c3b83947098ce0bd7c875a23f891 /gn/packages
parentfc284297def0b68c5a9fdd6c31cf9180b23fe73f (diff)
parent86fb35d3076401f899a5f3ae99403ecb25e3c260 (diff)
downloadguix-bioinformatics-b7853e6340adc3bc10cc48931db7c8f2ebe8c2d5.tar.gz
Merge branch 'master' of https://gitlab.com/genenetwork/guix-bioinformatics
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/gemma.scm2
-rw-r--r--gn/packages/genenetwork.scm12
-rw-r--r--gn/packages/javascript.scm175
-rw-r--r--gn/packages/python.scm34
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")