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-rw-r--r--gn/packages/bioinformatics.scm62
-rw-r--r--gn/packages/cwl.scm131
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."))))
+