gnu: Add GRIT.
* gnu/packages/bioinformatics.scm (grit): New variable.
This commit is contained in:
parent
ee3e157dec
commit
5854f6858b
|
@ -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")
|
||||
|
|
Loading…
Reference in New Issue