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authorpjotrp2016-03-01 05:43:18 +0000
committerpjotrp2016-03-01 05:43:18 +0000
commit520fb0f8ef40589738123f0129ccc34e1c756c9e (patch)
treed48292f58cb83fde699958c858317815b1bd20fd /gn/packages/genenetwork.scm
parent55915d466305bd00d15f605541ec926ca6fe0833 (diff)
parentf82b7c5b7ef5bdb9761e48761f683d62d3a05c48 (diff)
downloadguix-bioinformatics-520fb0f8ef40589738123f0129ccc34e1c756c9e.tar.gz
Merge branch 'master' into dennis
Diffstat (limited to 'gn/packages/genenetwork.scm')
-rw-r--r--gn/packages/genenetwork.scm35
1 files changed, 34 insertions, 1 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 2f755a6..033bf94 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -158,6 +158,7 @@
(propagated-inputs `( ;; propagated for development purposes
("python" ,python-2) ;; probably superfluous
("r" ,r)
+ ("r-wgcna" ,r-wgcna)
("redis" ,redis)
("mysql" ,mysql)
("gemma" ,gemma-git)
@@ -178,7 +179,7 @@
("python2-pandas" ,python2-pandas)
("python2-parallel" ,python2-parallel)
("python2-passlib" ,python2-passlib)
- ("python2-piddle" ,python2-piddle)
+ ("python2-piddle-gn" ,python2-piddle-gn)
("python2-redis" ,python2-redis)
("python2-requests" ,python2-requests)
("python2-rpy2" ,python2-rpy2)
@@ -202,3 +203,35 @@
;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
+
+(define-public genenetwork2-database-small
+ (let ((md5 "93e745e9c"))
+ (package
+ (name "genenetwork2-database-small")
+ (version "1.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip")
+ (file-name (string-append name "-" md5))
+ (sha256
+ (base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x"))))
+ (build-system trivial-build-system)
+ (native-inputs `(("unzip" ,unzip)
+ ("source" ,source)))
+
+ (arguments
+ `(#:modules ((guix build utils))
+ #:builder (begin
+ (use-modules (guix build utils))
+ (let ((source (assoc-ref %build-inputs "source"))
+ (unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip"))
+ )
+ (and (mkdir "db")
+ (zero? (system* unzip source "-d" "db"))
+ (chdir "db"))))))
+ (home-page "http://genenetwork.org/")
+ (synopsis "Small database to run on genenetwork")
+ (description "Genenetwork installation + database.")
+ (license license:agpl3+))))
+