gnu: Add GRIT.

* gnu/packages/bioinformatics.scm (grit): New variable.
This commit is contained in:
Ricardo Wurmus 2015-04-10 11:05:45 +02:00
parent ee3e157dec
commit 5854f6858b
1 changed files with 51 additions and 0 deletions

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@ -511,6 +511,57 @@ supports next-generation sequencing data in fasta/q and csfasta/q format from
Illumina, Roche 454, and the SOLiD platform.")
(license license:gpl3)))
(define-public grit
(package
(name "grit")
(version "2.0.2")
(source (origin
(method url-fetch)
(uri (string-append
"https://github.com/nboley/grit/archive/"
version ".tar.gz"))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"157in84dj70wimbind3x7sy1whs3h57qfgcnj2s6lrd38fbrb7mj"))))
(build-system python-build-system)
(arguments
`(#:python ,python-2
#:phases
(alist-cons-after
'unpack 'generate-from-cython-sources
(lambda* (#:key inputs outputs #:allow-other-keys)
;; Delete these C files to force fresh generation from pyx sources.
(delete-file "grit/sparsify_support_fns.c")
(delete-file "grit/call_peaks_support_fns.c")
(substitute* "setup.py"
(("Cython.Setup") "Cython.Build")
;; Add numpy include path to fix compilation
(("pyx\", \\]")
(string-append "pyx\", ], include_dirs = ['"
(assoc-ref inputs "python-numpy")
"/lib/python2.7/site-packages/numpy/core/include/"
"']"))) #t)
%standard-phases)))
(inputs
`(("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
("python-networkx" ,python2-networkx)))
(native-inputs
`(("python-cython" ,python2-cython)
("python-setuptools" ,python2-setuptools)))
(home-page "http://grit-bio.org")
(synopsis "Tool for integrative analysis of RNA-seq type assays")
(description
"GRIT is designed to use RNA-seq, TES, and TSS data to build and quantify
full length transcript models. When none of these data sources are available,
GRIT can be run by providing a candidate set of TES or TSS sites. In
addition, GRIT can merge in reference junctions and gene boundaries. GRIT can
also be run in quantification mode, where it uses a provided GTF file and just
estimates transcript expression.")
(license license:gpl3+)))
(define-public hisat
(package
(name "hisat")