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authorpjotrp2016-02-13 12:25:30 +0100
committerpjotrp2016-02-13 12:25:30 +0100
commitdf5f7651f94891effdcef4ec67af5a04c888713e (patch)
treed3f664a641b4b72bd3ab67310b98ad95cd61a615
parent0cf7d98524a94852b868b2f496e5324f132da5c0 (diff)
downloadguix-bioinformatics-df5f7651f94891effdcef4ec67af5a04c888713e.tar.gz
GN2: adding packages
-rw-r--r--gn/packages/bioinformatics.scm3
-rw-r--r--gn/packages/python.scm97
-rw-r--r--gn/packages/slurm.scm6
3 files changed, 103 insertions, 3 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index c576127..c796708 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -232,11 +232,13 @@ confidence region for the location of a putative QTL.")
(inputs `(
("mysql" ,mysql)
("nginx" ,nginx)
+ ("python2-flask" ,python2-flask)
("python2-jinja2" ,python2-jinja2)
("python2-sqlalchemy" ,python2-sqlalchemy)
("python2-setuptools" ,python2-setuptools)
("python2-scipy" ,python2-scipy)
;; looks like python-numarray is not needed
+ ("python2-mysqlclient" ,python2-mysqlclient)
("python2-numpy" ,python2-numpy)
("python2-pandas" ,python2-pandas)
("python2-passlib" ,python2-passlib)
@@ -244,6 +246,7 @@ confidence region for the location of a putative QTL.")
("python2-requests" ,python2-requests)
("python2-simplejson" ,python2-simplejson)
("python2-pyyaml" ,python2-pyyaml)
+ ("python-xlsxwriter" ,python-xlsxwriter)
;; python-yolk is not needed
("plink" ,plink)
("r-qtl" ,r-qtl)
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 8f53d54..41d6ee1 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -8,6 +8,7 @@
#:use-module (gnu packages gcc)
#:use-module (gnu packages ghostscript)
#:use-module (gnu packages glib)
+ #:use-module (gnu packages gnupg)
#:use-module (gnu packages gtk)
#:use-module (gnu packages icu4c)
#:use-module (gnu packages image)
@@ -41,6 +42,68 @@
#:use-module (guix build-system trivial)
#:use-module (srfi srfi-1))
+(define-public python-flask
+(package
+ (name "python-flask")
+ (version "0.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "Flask" version))
+ (sha256
+ (base32
+ "0wrkavjdjndknhp8ya8j850jq7a1cli4g5a93mg8nh1xz2gq50sc"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-setuptools" ,python-setuptools)
+ ; ("python-itsdangerous" ,python-itsdangerous)
+ ; ("python-jinja2" ,python-jinja2)
+ ; ("python-werkzeug" ,python-werkzeug)
+ ))
+ (propagated-inputs
+ `(
+ ("python-itsdangerous" ,python-itsdangerous)
+ ("python-jinja2" ,python-jinja2)
+ ("python-werkzeug" ,python-werkzeug)
+ ))
+
+ (arguments
+ `(#:tests? #f)) ; No tests
+ (home-page "http://github.com/mitsuhiko/flask/")
+ (synopsis
+ "A microframework based on Werkzeug, Jinja2 and good intentions")
+ (description
+ "A microframework based on Werkzeug, Jinja2 and good intentions")
+ (license license:bsd-3)))
+
+(define-public python2-flask
+ (package-with-python2 python-flask))
+
+(define-public python-xlsxwriter
+(package
+ (name "python-xlsxwriter")
+ (version "0.8.4")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "XlsxWriter" version))
+ (sha256
+ (base32
+ "0hv6bknnj9mlvvkdnlzycs0s97vrakmyh91ddb7ynjaqp8gl434z"))))
+ (build-system python-build-system)
+ (inputs
+ `(("python-setuptools" ,python-setuptools)))
+ (home-page
+ "https://github.com/jmcnamara/XlsxWriter")
+ (synopsis
+ "A Python module for creating Excel XLSX files.")
+ (description
+ "A Python module for creating Excel XLSX files.")
+ (license license:bsd-3)))
+
+(define-public python2-xlsxwriter
+ (package-with-python2 python-xlsxwriter))
+
(define-public python-rdflib-jsonld
(package
(name "python-rdflib-jsonld")
@@ -176,6 +239,40 @@ powerful language for representing information.")
(define-public python2-shellescape
(package-with-python2 python-shellescape))
+(define-public python-mysqlclient
+(package
+ (name "python-mysqlclient")
+ (version "1.3.7")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (pypi-uri "mysqlclient" version))
+ (sha256
+ (base32
+ "06qzgwk7j66k8ggx51i6wxx0f0zsppp7w4bh6gjd0cr9rfs86jn7"))))
+ (build-system python-build-system)
+ (inputs
+ `(
+ ("mysql" ,mysql)
+ ("python-nose" ,python-nose)
+ ("zlib" ,zlib)
+ ("openssl" ,openssl)
+ ("libgcrypt" ,libgcrypt)
+ ))
+ (propagated-inputs
+ `(("python-setuptools" ,python-setuptools)
+ ))
+ (arguments
+ `(#:tests? #f)) ; wants a running MySQL server
+ (home-page
+ "https://github.com/PyMySQL/mysqlclient-python")
+ (synopsis "Python interface to MySQL")
+ (description "Python interface to MySQL")
+ (license license:gpl3)))
+
+(define-public python2-mysqlclient
+ (package-with-python2 python-mysqlclient))
+
(define-public python2-numarray
(package
(name "python2-numarray")
diff --git a/gn/packages/slurm.scm b/gn/packages/slurm.scm
index 8f7ac1a..9e3d063 100644
--- a/gn/packages/slurm.scm
+++ b/gn/packages/slurm.scm
@@ -37,9 +37,9 @@
(define-public slurm-llnl
(package
- (name "slurm-llnl")
- (version "15-08-6-1")
- (source (origin
+ (name "slurm-llnl")
+ (version "15-08-6-1")
+ (source (origin
(method url-fetch)
(uri (string-append "https://github.com/SchedMD/slurm/archive/slurm-"
version ".tar.gz"))