gnu: Add PePr.
* gnu/packages/bioinformatics.scm (pepr): New variable.
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@ -4483,3 +4483,44 @@ Using a hidden Markov model, R/qtl allows to estimate genetic maps, to
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identify genotyping errors, and to perform single-QTL and two-QTL,
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identify genotyping errors, and to perform single-QTL and two-QTL,
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two-dimensional genome scans.")
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two-dimensional genome scans.")
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(license license:gpl3)))
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(license license:gpl3)))
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(define-public pepr
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(package
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(name "pepr")
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(version "1.0.9")
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(source (origin
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(method url-fetch)
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(uri (string-append "https://pypi.python.org/packages/source/P"
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"/PePr/PePr-" version ".tar.gz"))
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(sha256
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(base32
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"0qxjfdpl1b1y53nccws2d85f6k74zwmx8y8sd9rszcqhfayx6gdx"))))
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(build-system python-build-system)
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(arguments
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`(#:python ,python-2 ; python2 only
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#:tests? #f ; no tests included
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#:phases
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(modify-phases %standard-phases
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;; When setuptools is used a ".egg" archive is generated and
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;; installed. This makes it hard to actually run PePr. This issue
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;; has been reported upstream:
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;; https://github.com/shawnzhangyx/PePr/issues/9
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(add-after 'unpack 'disable-egg-generation
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(lambda _
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(substitute* "setup.py"
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(("from setuptools import setup")
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"from distutils.core import setup"))
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#t)))))
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(propagated-inputs
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`(("python2-numpy" ,python2-numpy)
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("python2-scipy" ,python2-scipy)
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("python2-pysam" ,python2-pysam)))
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(home-page "https://code.google.com/p/pepr-chip-seq/")
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(synopsis "Peak-calling and prioritization pipeline for ChIP-Seq data")
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(description
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"PePr is a ChIP-Seq peak calling or differential binding analysis tool
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that is primarily designed for data with biological replicates. It uses a
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negative binomial distribution to model the read counts among the samples in
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the same group, and look for consistent differences between ChIP and control
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group or two ChIP groups run under different conditions.")
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(license license:gpl3+)))
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