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gnu: Remove grit.
* gnu/packages/bioinformatics.scm (grit): Delete variable.
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@ -4025,48 +4025,6 @@ (define-public gemma
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genome-wide association studies}.")
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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 "2.0.5")
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/nboley/grit")
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(commit version)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1l5v8vfvfbrpmgnrvbrbv40d0arhxcnmxgv2f1mlcqfa3q6bkqm9"))))
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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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(modify-phases %standard-phases
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(add-after '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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#t)))))
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(inputs
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(list python2-scipy python2-numpy python2-pysam python2-networkx))
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(native-inputs
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(list python2-cython))
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;; The canonical <http://grit-bio.org> home page times out as of 2020-01-21.
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(home-page "https://github.com/nboley/grit")
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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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