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author | Pjotr Prins | 2016-03-09 11:22:34 -0500 |
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committer | Pjotr Prins | 2016-03-09 11:22:34 -0500 |
commit | 1b22d135eaf10407810cdc639d9af23efddb5330 (patch) | |
tree | e087a23758a6407001a92445f3c5b198613bb5b6 /gn/packages/genenetwork.scm | |
parent | 7f5437ebbe5980f9dbd6cad18bbebb2b0462cf7d (diff) | |
parent | d0a8f6e732ab4c0b1a93c3741f246c0ce812ef95 (diff) | |
download | guix-bioinformatics-1b22d135eaf10407810cdc639d9af23efddb5330.tar.gz |
Merge branch 'master' of github.com:roelj/guix-bioinformatics into roelj
Diffstat (limited to 'gn/packages/genenetwork.scm')
-rw-r--r-- | gn/packages/genenetwork.scm | 21 |
1 files changed, 18 insertions, 3 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index fdcbb7f..3d62d55 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -154,10 +154,14 @@ (sha256 (base32 "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618")))) + (inputs `( + ("r-wgcna" ,r-wgcna) + ("r-qtl" ,r-qtl))) (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous ("r" ,r) ("r-wgcna" ,r-wgcna) + ("r-qtl" ,r-qtl) ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) @@ -181,6 +185,7 @@ ("python2-passlib" ,python2-passlib) ("python2-piddle-gn" ,python2-piddle-gn) ("python2-redis" ,python2-redis) + ("python2-pil" ,python2-pil) ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) ("python2-scipy" ,python2-scipy) @@ -190,7 +195,6 @@ ;; python-yolk is not needed ("plink" ,plink) ("qtlreaper" ,qtlreaper) - ("r-qtl" ,r-qtl) )) (build-system python-build-system) (arguments @@ -199,9 +203,20 @@ (modify-phases %standard-phases (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) - (let* ((datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" ))) + (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")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) + ) + (substitute* '("etc/default_settings.py") - (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))))))) + (("^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") |