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authorPjotr Prins2016-03-09 11:22:34 -0500
committerPjotr Prins2016-03-09 11:22:34 -0500
commit1b22d135eaf10407810cdc639d9af23efddb5330 (patch)
treee087a23758a6407001a92445f3c5b198613bb5b6 /gn/packages/genenetwork.scm
parent7f5437ebbe5980f9dbd6cad18bbebb2b0462cf7d (diff)
parentd0a8f6e732ab4c0b1a93c3741f246c0ce812ef95 (diff)
downloadguix-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.scm21
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")