gnu: seqmagick: Update to 0.7.0.
* gnu/packages/bioinformatics.scm (seqmagick): Update to 0.7.0. Use python-3. [arguments]: Remove replacement phase for check. [inputs]: Add biopython. Remove python2-biopython-1.66. (python2-biopython-1.66): Remove variable.
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@ -790,20 +790,6 @@ into separate processes; and more.")
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(define-public python2-biopython
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(package-with-python2 python-biopython))
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;; An outdated version of biopython is required for seqmagick, see
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;; https://github.com/fhcrc/seqmagick/issues/59
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;; When that issue has been resolved this package should be removed.
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(define python2-biopython-1.66
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(package
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(inherit python2-biopython)
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(version "1.66")
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(source (origin
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(method url-fetch)
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(uri (pypi-uri "biopython" version))
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(sha256
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(base32
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"1gdv92593klimg22icf5j9by7xiq86jnwzkpz4abaa05ylkdf6hp"))))))
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(define-public bpp-core
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;; The last release was in 2014 and the recommended way to install from source
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;; is to clone the git repository, so we do this.
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@ -5391,7 +5377,7 @@ bioinformatics file formats, sequence alignment, and more.")
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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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(version "0.7.0")
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(source
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(origin
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(method url-fetch)
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@ -5400,25 +5386,12 @@ bioinformatics file formats, sequence alignment, and more.")
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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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"12bfyp8nqi0hd36rmj450aygafp01qy3hkbvlwn3bk39pyjjkgg5"))))
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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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;; biopython-1.66 is required due to
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;; https://github.com/fhcrc/seqmagick/issues/59
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;; When that issue is resolved the 'python2-biopython-1.66' package
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;; should be removed.
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`(("python-biopython" ,python2-biopython-1.66)))
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`(("python-biopython" ,python-biopython)))
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(native-inputs
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`(("python-nose" ,python2-nose)))
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`(("python-nose" ,python-nose)))
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(home-page "https://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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