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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-04-10 11:05:45 +0200
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-04-10 14:35:48 +0200
commit5854f6858bc4ed61ebc03a0a887661eadcbea640 (patch)
tree492aecd52ee8cecfacf8de5b8a17419777e1557d /gnu/packages
parentee3e157dec3512778502f20538c581f5e28d63fe (diff)
downloadpatches-5854f6858bc4ed61ebc03a0a887661eadcbea640.tar
patches-5854f6858bc4ed61ebc03a0a887661eadcbea640.tar.gz
gnu: Add GRIT.
* gnu/packages/bioinformatics.scm (grit): New variable.
Diffstat (limited to 'gnu/packages')
-rw-r--r--gnu/packages/bioinformatics.scm51
1 files changed, 51 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b122b6d83d..e143fb2c55 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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")