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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 51 |
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") |