diff options
| -rw-r--r-- | gn/packages/gemma.scm | 2 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 12 | ||||
| -rw-r--r-- | gn/packages/javascript.scm | 175 | ||||
| -rw-r--r-- | gn/packages/python.scm | 34 |
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") |