diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 62 | ||||
| -rw-r--r-- | gn/packages/cwl.scm | 131 |
2 files changed, 193 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm new file mode 100644 index 0000000..8197d33 --- /dev/null +++ b/gn/packages/bioinformatics.scm @@ -0,0 +1,62 @@ +;; Bioinformatics module + +(define-module (gn packages bioinformatics) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils) + #:use-module (guix download) + #:use-module (guix git-download) + #:use-module (guix build-system gnu) + #:use-module (guix build-system cmake) + #:use-module (guix build-system perl) + #:use-module (guix build-system python) + #:use-module (guix build-system ruby) + #:use-module (guix build-system r) + #:use-module (guix build-system trivial) + #:use-module (gnu packages) + #:use-module (gnu packages algebra) + #:use-module (gnu packages base) + #:use-module (gnu packages boost) + #:use-module (gnu packages compression) + #:use-module (gnu packages cpio) + #:use-module (gnu packages file) + #:use-module (gnu packages java) + #:use-module (gnu packages linux) + #:use-module (gnu packages machine-learning) + #:use-module (gnu packages maths) + #:use-module (gnu packages ncurses) + #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages popt) + #:use-module (gnu packages protobuf) + #:use-module (gnu packages python) + #:use-module (gnu packages ruby) + #:use-module (gnu packages statistics) + #:use-module (gnu packages tbb) + #:use-module (gnu packages textutils) + #:use-module (gnu packages vim) + #:use-module (gnu packages web) + #:use-module (gnu packages xml) + #:use-module (gnu packages zip) + #:use-module (srfi srfi-1)) + +(define-public r-qtl + (package + (name "r-qtl") + (version "1.37-11") + (source + (origin + (method url-fetch) + (uri (string-append + "mirror://cran/src/contrib/qtl_" + version ".tar.gz")) + (sha256 + (base32 + "0h20d36mww7ljp51pfs66xq33yq4b4fwq9nsh02dpmfhlaxgx1xi")))) + (build-system r-build-system) + (home-page "http://www.rqtl.org") + (synopsis "Tools for Analyzing QTL Experiments") + (description "Bio-statistics library for analysis of experimental +crosses to identify genes (called quantitative trait loci, QTLs) +contributing to variation in quantitative traits.") + (license license:gpl3+))) diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm new file mode 100644 index 0000000..e158f68 --- /dev/null +++ b/gn/packages/cwl.scm @@ -0,0 +1,131 @@ +;; Experimental packaging for the Common Workflow Language (started by Bruno) + +(define-module (gn packages cwl) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (gnu packages) + #:use-module (gnu packages python) + #:use-module (guix download) + #:use-module (guix packages) + #:use-module (guix git-download) + #:use-module (guix utils) + #:use-module (guix build-system gnu) + #:use-module (guix build-system python) + #:use-module (guix build-system trivial) + #:use-module (srfi srfi-1)) + +(define-public python-cwltool + (package + (name "python-cwltool") + (version "1.0.20150916041152") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/c/cwltool/cwltool-" + version + ".tar.gz")) + (sha256 + (base32 + "1kqxc6nvq4nr8qdv39ycdi6fhzaipgjpmbghsz94ij6jhf5r3dq2")))) + (build-system python-build-system) + (inputs + `(("python-setuptools" ,python-setuptools))) + (home-page + "https://github.com/common-workflow-language/common-workflow-language") + (synopsis + "Common workflow language reference implementation") + (description + "Common workflow language reference implementation") + (license asl2.0))) + +(define-public python-rdflib-jsonld + (package + (name "python-rdflib-jsonld") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/r/rdflib-jsonld/rdflib-jsonld-" + version + ".tar.gz")) + (sha256 + (base32 + "121a876k49xl85jvikyh4hzvm34456ikw66cra5dfyr15br1qjll")))) + (build-system python-build-system) + (inputs + `(("python-setuptools" ,python-setuptools))) + (home-page + "https://github.com/RDFLib/rdflib-jsonld") + (synopsis + "rdflib extension adding JSON-LD parser and serializer") + (description + "rdflib extension adding JSON-LD parser and serializer") + (license bsd-3))) + +(define-public python-schema-salad + (package + (name "python-schema-salad") + (version "1.0.2") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/s/schema-salad/schema-salad-" + version + ".tar.gz")) + (sha256 + (base32 + "09axiiirq73s1cs21n8mkdslaca2gxc2mlayyl6yiaq98cfgfh37")))) + (build-system python-build-system) + (arguments `(#:tests? #f)) ;; No tests. + (inputs + `(("python-cython" ,python-cython) + ("python-setuptools" ,python-setuptools) + ("python-rdflib-jsonld" ,python-rdflib-jsonld) + ("python-rdflib" ,python-rdflib) + ("python-mistune" ,python-mistune))) + (propagated-inputs + `(("python-rdflib" ,python-rdflib))) + (native-inputs + `(("python-rdflib" ,python-rdflib))) + (home-page + "https://github.com/common-workflow-language/common-workflow-language") + (synopsis + "Schema Annotations for Linked Avro Data (SALAD)") + (description + "Schema Annotations for Linked Avro Data (SALAD)") + (license asl2.0))) + +(define-public python-rdflib + (package + (name "python-rdflib") + (version "4.2.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://pypi.python.org/packages/source/r/rdflib/rdflib-" + version + ".tar.gz")) + (patches + ;; The patch has no effect under Python 3. + (list (search-patch "python2-rdflib-drop-sparqlwrapper.patch"))) + (sha256 + (base32 + "1h3f8yl9frjz8rsykjdjk83qsrcvld3qa7pkzh69s91h97ydl83l")))) + (build-system python-build-system) + (inputs + `(("python-html5lib" ,python-html5lib) + ("python-isodate" ,python-isodate) + ("python-pyparsing" ,python-pyparsing) + ("python-setuptools" ,python-setuptools))) + (home-page "https://github.com/RDFLib/rdflib") + (synopsis + "Python RDF library") + (description + "RDFLib is a Python library for working with RDF, a simple yet +powerful language for representing information.") + (license (non-copyleft "file://LICENSE" + "See LICENSE in the distribution.")))) + |