From df5f7651f94891effdcef4ec67af5a04c888713e Mon Sep 17 00:00:00 2001 From: pjotrp Date: Sat, 13 Feb 2016 12:25:30 +0100 Subject: GN2: adding packages --- gn/packages/bioinformatics.scm | 3 ++ gn/packages/python.scm | 97 ++++++++++++++++++++++++++++++++++++++++++ gn/packages/slurm.scm | 6 +-- 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")) -- cgit v1.2.3