gnu: Add python-bx-python.
* gnu/packages/bioinformatics.scm (python-bx-python): New variable. (python2-bx-python): Define in terms of python-bx-python.
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@ -1474,9 +1474,9 @@ the original BWA alignment program and shares the genome index structure as
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well as many of the command line options.")
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well as many of the command line options.")
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(license license:gpl3+)))
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(license license:gpl3+)))
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(define-public python2-bx-python
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(define-public python-bx-python
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(package
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(package
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(name "python2-bx-python")
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(name "python-bx-python")
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(version "0.8.2")
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(version "0.8.2")
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(source (origin
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(source (origin
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(method url-fetch)
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(method url-fetch)
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@ -1485,18 +1485,17 @@ well as many of the command line options.")
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(base32
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(base32
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"11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs"))))
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"11kksg2rbzihpmcid823xvg42xi88m7sz58rzk29abybkxy0rszs"))))
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(build-system python-build-system)
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(build-system python-build-system)
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(arguments
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;; Tests fail because test data are not included
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`(#:tests? #f ;tests fail because test data are not included
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(arguments '(#:tests? #f))
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#:python ,python-2))
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(propagated-inputs
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(propagated-inputs
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`(("python-numpy" ,python2-numpy)
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`(("python-numpy" ,python-numpy)
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("python-six" ,python2-six)))
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("python-six" ,python-six)))
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(inputs
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(inputs
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`(("zlib" ,zlib)))
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`(("zlib" ,zlib)))
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(native-inputs
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(native-inputs
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`(("python-lzo" ,python2-lzo)
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`(("python-lzo" ,python-lzo)
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("python-nose" ,python2-nose)
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("python-nose" ,python-nose)
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("python-cython" ,python2-cython)))
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("python-cython" ,python-cython)))
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(home-page "https://github.com/bxlab/bx-python")
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(home-page "https://github.com/bxlab/bx-python")
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(synopsis "Tools for manipulating biological data")
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(synopsis "Tools for manipulating biological data")
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(description
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(description
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@ -1504,6 +1503,9 @@ well as many of the command line options.")
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multiple sequence alignments.")
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multiple sequence alignments.")
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(license license:expat)))
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(license license:expat)))
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(define-public python2-bx-python
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(package-with-python2 python-bx-python))
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(define-public python-pysam
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(define-public python-pysam
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(package
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(package
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(name "python-pysam")
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(name "python-pysam")
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