gnu: Add python-screed.
* gnu/packages/bioinformatics.scm (python-screed, python2-screed): New variables.
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@ -3359,6 +3359,44 @@ optimize the sequencing depth, or to screen multiple libraries to avoid low
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complexity samples.")
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(license license:gpl3+)))
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(define-public python-screed
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(package
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(name "python-screed")
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(version "0.9")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "screed" version))
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(sha256
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(base32
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"18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))))
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(build-system python-build-system)
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(arguments
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`(#:phases
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(modify-phases %standard-phases
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(replace 'check
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(lambda _
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(setenv "PYTHONPATH"
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(string-append (getenv "PYTHONPATH") ":."))
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(zero? (system* "nosetests" "--attr" "!known_failing")))))))
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(native-inputs
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`(("python-nose" ,python-nose)))
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(inputs
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`(("python-bz2file" ,python-bz2file)))
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(home-page "http://github.com/dib-lab/screed/")
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(synopsis "Short read sequence database utilities")
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(description "Screed parses FASTA and FASTQ files and generates databases.
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Values such as sequence name, sequence description, sequence quality and the
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sequence itself can be retrieved from these databases.")
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(license license:bsd-3)))
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(define-public python2-screed
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(let ((base (package-with-python2 (strip-python2-variant python-screed))))
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(package
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(inherit base)
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(native-inputs `(("python2-setuptools" ,python2-setuptools)
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,@(package-native-inputs base))))))
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(define-public sra-tools
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(package
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(name "sra-tools")
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