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| author | pjotrp | 2016-03-05 16:07:32 +0000 |
|---|---|---|
| committer | pjotrp | 2016-03-05 16:07:32 +0000 |
| commit | a4a9f2eec7a770a52bbeda64169ba9e3b1ff2583 (patch) | |
| tree | 12012e10e7b0ecaedc48ed5b6150e37e8cc5bef2 /gn/packages/genenetwork.scm | |
| parent | 570d7b6118739bb76b6d32881e9ef45e50a9e3ae (diff) | |
| download | guix-bioinformatics-a4a9f2eec7a770a52bbeda64169ba9e3b1ff2583.tar.gz | |
Guix paths to the tools
Diffstat (limited to 'gn/packages/genenetwork.scm')
| -rw-r--r-- | gn/packages/genenetwork.scm | 20 |
1 files changed, 17 insertions, 3 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index fdcbb7f..c952792 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) @@ -190,7 +194,6 @@ ;; python-yolk is not needed ("plink" ,plink) ("qtlreaper" ,qtlreaper) - ("r-qtl" ,r-qtl) )) (build-system python-build-system) (arguments @@ -199,9 +202,20 @@ (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") |