diff options
| 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 | |
| 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')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 14 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 9 |
2 files changed, 10 insertions, 13 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index c1b22fd..c04c6c8 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -840,8 +840,8 @@ confidence region for the location of a putative QTL.") (inputs `(("zlib" ,zlib) ("openblas" ,openblas) - ("atlas" ,atlas) - ("lapack" ,lapack) + ;; ("atlas" ,atlas) + ;; ("lapack" ,lapack) ("gfortran" ,gfortran) )) (native-inputs @@ -861,7 +861,7 @@ subsequent visualization, annotation and storage of results.") (license (list license:gpl2 license:lgpl2.1+)))) (define-public plink-ng - (let ((commit "516d730f9")) + (let ((commit "6ab6ecf81e904b7db76454422ea59baae437d961")) (package (name "plink-ng") (version (string-append "1.90b3-" commit )) @@ -873,8 +873,8 @@ subsequent visualization, annotation and storage of results.") (file-name (string-append name "-" commit)) (sha256 (base32 - "0cv824wkdml9h9imsc30s2x3l8g65j44cpjbr1ydkk49g5qmf580")) - (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch"))))) + "0djnfcr3lm6839lkglpq1p4w09zlgv68p618c2i5dng4jhwji94k")))) + ;;; (patches (list (search-patch "plink-ng-Makefile-zlib-git.patch")) (build-system gnu-build-system) (arguments '(#:tests? #f ;no "check" target @@ -894,8 +894,8 @@ subsequent visualization, annotation and storage of results.") (inputs `(("zlib" ,zlib) ("openblas" ,openblas) - ("atlas" ,atlas) - ("lapack" ,lapack) + ;; ("atlas" ,atlas) + ;; ("lapack" ,lapack) ("gfortran" ,gfortran) )) (native-inputs 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" )) ) )))) |