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authorpjotrp2016-03-05 16:07:32 +0000
committerpjotrp2016-03-05 16:07:32 +0000
commita4a9f2eec7a770a52bbeda64169ba9e3b1ff2583 (patch)
tree12012e10e7b0ecaedc48ed5b6150e37e8cc5bef2 /gn/packages
parent570d7b6118739bb76b6d32881e9ef45e50a9e3ae (diff)
downloadguix-bioinformatics-a4a9f2eec7a770a52bbeda64169ba9e3b1ff2583.tar.gz
Guix paths to the tools
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm2
-rw-r--r--gn/packages/genenetwork.scm20
-rw-r--r--gn/packages/python.scm2
3 files changed, 20 insertions, 4 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 295a2b3..c04c928 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -305,8 +305,8 @@ length of a short-read sequencing alignment.")
(propagated-inputs
`( ;; ("r-annotationdbi" ,r-annotationdbi)
; ("r-biocparallel" ,r-biocparallel)
- ("r-dynamictreecut" ,r-dynamictreecut)
("r-doparallel" ,r-doparallel)
+ ("r-dynamictreecut" ,r-dynamictreecut)
("r-fastcluster" ,r-fastcluster)
("r-foreach" ,r-foreach)
("r-go-db" ,r-go-db)
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")
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 6fff9a3..8157c0b 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -432,6 +432,8 @@ version ".tgz"))
(build-system python-build-system)
(native-inputs
`(("python2-setuptools" ,python2-setuptools)))
+ (propagated-inputs
+ `(("python2-pil" ,python2-pil)))
(arguments
`(
#:python ,python-2