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