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| author | Pjotr Prins | 2016-08-14 02:16:30 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2016-08-14 02:16:30 -0500 |
| commit | b3394e07071d11674cc796e6a4a3de5fc4634a78 (patch) | |
| tree | a5b582c13e1c8ac796a7fc0ac8bca3a6672e1981 /gn/packages/genenetwork.scm | |
| parent | 71fd1cbbd9fb97b6893f707123f843a9d9ab7522 (diff) | |
| download | guix-bioinformatics-b3394e07071d11674cc796e6a4a3de5fc4634a78.tar.gz | |
Getting GN2 ready for new build - plink-ng is disabled and should not be built with atlas and lapack (FIXME)
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 9 |
1 files changed, 3 insertions, 6 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4f3d356..10f0a26 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -164,7 +164,7 @@ ("gemma" ,gemma-git) ("genenetwork2-files-small" ,genenetwork2-files-small) ("pylmm-gn2" ,pylmm-gn2) - ("plink2" ,plink-ng) + ;; ("plink2" ,plink-ng) disabled - FIXME ("nginx" ,nginx) ("python2-flask" ,python2-flask) ("python2-htmlgen-gn" ,python2-htmlgen-gn) @@ -173,7 +173,6 @@ ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) ("python2-setuptools" ,python2-setuptools) ("python2-scipy" ,python2-scipy) - ;; looks like python-numarray is not needed ("python2-mysqlclient" ,python2-mysqlclient) ("python2-numarray" ,python2-numarray) ("python2-numpy" ,python2-numpy) @@ -189,8 +188,6 @@ ("python2-simplejson" ,python2-simplejson) ("python2-pyyaml" ,python2-pyyaml) ("python2-xlsxwriter" ,python2-xlsxwriter) - ;; python-yolk is not needed - ("plink" ,plink) ("qtlreaper" ,qtlreaper) )) (build-system python-build-system) @@ -203,14 +200,14 @@ (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 "plink2") "/bin/plink2")) + ;; (plink2cmd (string-append (assoc-ref inputs "plink2") "/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" )) + ;; (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) ) )))) |