From 117a3192ab26d8fd1caeca648533cc58ed420f06 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Tue, 27 Oct 2020 15:21:07 +0300 Subject: gn: Delete genenetwork3 package * gn/packages/genenetwork.scm (genenetwork3): Delete it. The python3 version of genenetwork2 is already packaged as python3-genenetwork2. --- gn/packages/genenetwork.scm | 132 -------------------------------------------- 1 file changed, 132 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 7946f70..6641ae6 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -591,138 +591,6 @@ Graphical Fragment Assembly} files and related formats.") written in C") (license license:agpl3+)))) -(define-public genenetwork3 - (let (;; (commit "1538ffd33af19e6ac922b4ee85fe701408968dfd") - (commit "5bff4f49dffb4ac982d36cd0d39e0a9ec6bc66e9")) - (package - (name "genenetwork3") - (version (string-append "2.10rc5-" (string-take commit 7) )) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/fredmanglis/genenetwork2.git") - ;; (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git") - ;; (url "https://github.com/genenetwork/genenetwork2_diet.git") - (commit commit))) - (file-name (string-append name "-" version)) - (sha256 - (base32 - "0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di" - ;; "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz" - )))) - (propagated-inputs ;; propagated for development purposes - `(;; Agnostic to Python - ("r" ,r) - ("git" ,git) - ("vim" ,vim) - ("grep" ,grep) - ("which" ,which) - ("r-ctl" ,r-ctl) - ("r-qtl" ,r-qtl) - ("redis" ,redis) - ("mariadb" ,mariadb) - ("nginx" ,nginx) - ("r-wgcna" ,r-wgcna) - ;; ("r-phewas" ,r-phewas) - ("coreutils" ,coreutils) - ("gemma" ,gemma-gn2-git) - ("plink-ng-gn" ,plink-ng-gn) - ("python-lxml" ,python-lxml) ;; used for the tests - ("gemma-wrapper" ,gemma-wrapper) - ("python-unittest" ,python-unittest2) ;; used for the tests - ("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) - ("javascript-chroma" ,javascript-chroma) - ;; With Python3 support - ("gunicorn" ,gunicorn) - ("python-rpy2" ,python-rpy2) - ("python-flask" ,python-flask) - ("python-scipy" ,python-scipy) - ("python-numpy" ,python-numpy) - ("python-redis" ,python-redis) - ("python-scipy" ,python-scipy) - ("python-pillow" ,python-pillow) - ("python-reaper" ,python-reaper) - ("python-pyyaml" ,python-pyyaml) - ("python-jinja2" ,python-jinja2) - ("python-pandas" ,python-pandas) - ("python-htmlgen" ,python-htmlgen) - ("python-passlib" ,python-passlib) - ("python-wrapper" ,python-wrapper) - ("python-requests" ,python-requests) - ("python-cssselect" ,python-cssselect) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-setuptools" ,python-setuptools) - ("python-simplejson" ,python-simplejson) - ("python-xlsxwriter" ,python-xlsxwriter) - ("python-mysqlclient" ,python-mysqlclient) - ("python-elasticsearch" ,python-elasticsearch) - ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) - - ;; Without Python3 support - ;; ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program - ;; ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program - ;; ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT) - ;; ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions - )) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases - %standard-phases - (delete 'reset-gzip-timestamps) - (add-after - 'unpack 'fix-paths-scripts - (lambda _ - (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which"))) - #t)) - (add-before - 'install 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (let* ((datafiles - (string-append - (assoc-ref inputs "genenetwork2-files-small") - "/share/genenetwork2" )) - ;; (pylmmcmd - ;; (string-append - ;; (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) - (plink2cmd - (string-append - (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) - (gemmacmd - (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) - - (substitute* - '("etc/default_settings.py") - (("^GENENETWORK_FILES +=.*") - (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) - (("^PYLMM_COMMAND =.*") - (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) - (("^PLINK_COMMAND =.*") - (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) - (("^GEMMA_COMMAND =.*") - (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n"))))))) - #:tests? #f)) ; no 'setup.py test' - (home-page "http://genenetwork.org/") - (synopsis "Full genenetwork services") - (description "Genenetwork installation sumo.") - (license license:agpl3+)))) (define-public genenetwork1 (let ((commit "acf65ac9ae4be395c07c1629758f7408bf4eab5f") ; June 3, 2020 -- cgit v1.2.3