gnu: Add python-screed.

* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
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Ben Woodcroft 2016-06-14 15:53:33 +10:00
parent 095b7fea44
commit 9ded145717
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@ -3359,6 +3359,44 @@ optimize the sequencing depth, or to screen multiple libraries to avoid low
complexity samples.")
(license license:gpl3+)))
(define-public python-screed
(package
(name "python-screed")
(version "0.9")
(source
(origin
(method url-fetch)
(uri (pypi-uri "screed" version))
(sha256
(base32
"18czszp9fkx3j6jr7y5kp6dfialscgddk05mw1zkhh2zhn0jd8i0"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(replace 'check
(lambda _
(setenv "PYTHONPATH"
(string-append (getenv "PYTHONPATH") ":."))
(zero? (system* "nosetests" "--attr" "!known_failing")))))))
(native-inputs
`(("python-nose" ,python-nose)))
(inputs
`(("python-bz2file" ,python-bz2file)))
(home-page "http://github.com/dib-lab/screed/")
(synopsis "Short read sequence database utilities")
(description "Screed parses FASTA and FASTQ files and generates databases.
Values such as sequence name, sequence description, sequence quality and the
sequence itself can be retrieved from these databases.")
(license license:bsd-3)))
(define-public python2-screed
(let ((base (package-with-python2 (strip-python2-variant python-screed))))
(package
(inherit base)
(native-inputs `(("python2-setuptools" ,python2-setuptools)
,@(package-native-inputs base))))))
(define-public sra-tools
(package
(name "sra-tools")