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-rw-r--r--gn/packages/bioinformatics.scm51
1 files changed, 51 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c24eb61..61ab0a1 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -22,6 +22,7 @@
#:use-module (gnu packages databases)
#:use-module (gnu packages cpio)
#:use-module (gnu packages file)
+ #:use-module (gnu packages graphviz)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
@@ -156,6 +157,56 @@ confidence region for the location of a putative QTL.")
(license license:gpl2)))
+(define-public genenetwork1
+ (let ((commit "d622c803b"))
+ (package
+ (name "genenetwork1")
+ (version (string-append "1.0-" commit ))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/pjotrp/genenetwork.git")
+ ;; (url "https://github.com/pjotrp/genenetwork.git")
+ (commit commit)))
+ (file-name (string-append name "-" commit))
+ (sha256
+ (base32
+ "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjha"))))
+ (propagated-inputs `(
+ ("python" ,python-2) ;; probably superfluous
+ ("r" ,r)
+ ))
+ (inputs `(
+ ;; graphviz-2.22.2 htmlgen json numarray-1.5.2 piddle PIL pp-1.5.7 pyx pyXLWriter svg
+ ("mysql" ,mysql)
+ ("nginx" ,nginx)
+ ("graphviz" ,graphviz)
+ ; ("python2-jinja2" ,python2-jinja2)
+ ; ("python2-sqlalchemy" ,python2-sqlalchemy)
+ ; ("python2-setuptools" ,python2-setuptools)
+ ; ("python2-scipy" ,python2-scipy)
+ ;; looks like python-numarray is not needed
+ ; ("python2-numpy" ,python2-numpy)
+ ; ("python2-pandas" ,python2-pandas)
+ ; ("python2-passlib" ,python2-passlib)
+ ; ("python2-redis" ,python2-redis)
+ ; ("python2-requests" ,python2-requests)
+ ; ("python2-simplejson" ,python2-simplejson)
+ ; ("python2-pyyaml" ,python2-pyyaml)
+ ;; python-yolk is not needed
+ ("python2-pil" ,python2-pil)
+ ("plink" ,plink) ;; gn1
+ ; ("r-qtl" ,r-qtl)
+ ))
+ (build-system python-build-system)
+ (arguments
+ `(#:python ,python-2
+ #:tests? #f)) ; no 'setup.py test'
+ (home-page "http://genenetwork.org/")
+ (synopsis "Full genenetwork services")
+ (description "Genenetwork installation sumo.")
+ (license license:agpl3+))))
+
(define-public genenetwork2
(let ((commit "9e9475053"))
(package