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| -rw-r--r-- | gn/packages/genenetwork.scm | 131 |
1 files changed, 131 insertions, 0 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 14b7945..5217f65 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -353,3 +353,134 @@ location of a putative QTL.") (synopsis "Small database to run on genenetwork") (description "Genenetwork installation + database.") (license license:agpl3+)))) + + +(define-public genenetwork3 + (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")) + (package + (name "genenetwork3") + (version (string-append "2.10rc5-" (string-take commit 7) )) + (source (origin + (method git-fetch) + (uri (git-reference + (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 + "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) + ("mysql" ,mysql) + ("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) + + + ;; 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-pyyaml" ,python-pyyaml) + ("python-jinja2" ,python-jinja2) + ("python-pandas" ,python-pandas) + ("python-passlib" ,python-passlib) + ("python-requests" ,python-requests) + ("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 + ("qtlreaper" ,qtlreaper) ;; Run as an external program + ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program + ("python2-pil1" ,python2-pil1) ; should move to pillow some day. Run as external python2 program + ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT) + ("python2-piddle-gn" ,python2-piddle-gn) ;; Run as external python2 program + ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions + + + ;; Removed packages + ;; ("python2-mechanize" ,python2-mechanize) + ;; ("python2-parallel" ,python2-parallel) + )) + (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+)))) |