gnu: Add seqmagick.
* gnu/packages/bioinformatics.scm (seqmagick): New variable.
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@ -2552,6 +2552,44 @@ manipulation, online and indexed string search, efficient I/O of
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bioinformatics file formats, sequence alignment, and more.")
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(license license:bsd-3)))
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(define-public seqmagick
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(package
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(name "seqmagick")
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(version "0.6.1")
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(source
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(origin
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(method url-fetch)
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(uri (string-append
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"https://pypi.python.org/packages/source/s/seqmagick/seqmagick-"
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version ".tar.gz"))
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(sha256
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(base32
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"0cgn477n74gsl4qdaakrrhi953kcsd4q3ivk2lr18x74s3g4ma1d"))))
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(build-system python-build-system)
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(arguments
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;; python2 only, see https://github.com/fhcrc/seqmagick/issues/56
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`(#:python ,python-2
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#:phases
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(modify-phases %standard-phases
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;; Current test in setup.py does not work as of 0.6.1,
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;; so use nose to run tests instead for now. See
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;; https://github.com/fhcrc/seqmagick/issues/55
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(replace 'check (lambda _ (zero? (system* "nosetests")))))))
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(inputs
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`(("python-biopython" ,python2-biopython)))
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(native-inputs
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`(("python-setuptools" ,python2-setuptools)
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("python-nose" ,python2-nose)))
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(home-page "http://github.com/fhcrc/seqmagick")
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(synopsis "Tools for converting and modifying sequence files")
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(description
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"Bioinformaticians often have to convert sequence files between formats
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and do little manipulations on them, and it's not worth writing scripts for
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that. Seqmagick is a utility to expose the file format conversion in
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BioPython in a convenient way. Instead of having a big mess of scripts, there
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is one that takes arguments.")
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(license license:gpl3)))
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(define-public star
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(package
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(name "star")
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