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authorpjotrp2018-03-20 11:13:56 +0000
committerpjotrp2018-03-20 11:13:56 +0000
commit84dd8cebae9eefdb7d7f9ca43e53b3ddfc295eb1 (patch)
treeaaa09ca5cf459f762a1eb53c65dc98c5801ff3cd /gn/packages
parent50dbb901666064a9925e6053090ef59419ad1ce5 (diff)
downloadguix-bioinformatics-84dd8cebae9eefdb7d7f9ca43e53b3ddfc295eb1.tar.gz
Adding GN python packages for testing
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/genenetwork.scm5
-rw-r--r--gn/packages/python.scm21
2 files changed, 26 insertions, 0 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index d9696a3..14b7945 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -19,6 +19,7 @@
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
+ #:use-module (gnu packages check)
#:use-module (gnu packages databases)
#:use-module (gnu packages cpio)
#:use-module (gn packages elixir)
@@ -202,6 +203,7 @@ location of a putative QTL.")
("nginx" ,nginx)
("python2-flask" ,python2-flask)
("gunicorn" ,gunicorn)
+ ("python2-cssselect" ,python2-cssselect)
("python2-elasticsearch" ,python2-elasticsearch)
("python2-htmlgen-gn" ,python2-htmlgen-gn)
("python2-jinja2" ,python2-jinja2)
@@ -209,12 +211,14 @@ location of a putative QTL.")
("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)
("python2-setuptools" ,python2-setuptools)
("python2-scipy" ,python2-scipy)
+ ("python2-lxml" ,python2-lxml)
("python2-mechanize" ,python2-mechanize)
("python2-mysqlclient" ,python2-mysqlclient)
("python2-numarray" ,python2-numarray)
("python2-numpy" ,python2-numpy)
("python2-pandas" ,python2-pandas)
("python2-parallel" ,python2-parallel)
+ ("python2-parameterized" ,python2-parameterized)
("python2-passlib" ,python2-passlib)
("python2-piddle-gn" ,python2-piddle-gn)
("python2-redis" ,python2-redis)
@@ -225,6 +229,7 @@ location of a putative QTL.")
("python2-scipy" ,python2-scipy)
("python2-simplejson" ,python2-simplejson)
("python2-pyyaml" ,python2-pyyaml)
+ ("python2-unittest2" ,python2-unittest2)
("python2-xlsxwriter" ,python2-xlsxwriter)
("qtlreaper" ,qtlreaper)
("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 9601b3c..a6a99c6 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -44,6 +44,27 @@
#:use-module (guix build-system trivial)
#:use-module (srfi srfi-1))
+(define-public python-pyvcf
+ (package
+ (name "python-pyvcf")
+ (version "0.6.8")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "pyvcf" version))
+ (sha256
+ (base32
+ "1ngryr12d3izmhmwplc46xhyj9i7yhrpm90xnsd2578p7m8p5n79"))))
+ (build-system python-build-system)
+ (home-page
+ "https://github.com/jamescasbon/PyVCF")
+ (synopsis
+ "Variant Call Format (VCF) parser for Python")
+ (description
+ "Variant Call Format (VCF) parser for Python")
+ (license #f)))
+
+
(define-public python-elasticsearch
(package
(name "python-elasticsearch")