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gnu: htseq: Update to 0.9.1. 

* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package.  Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
This commit is contained in:
Ben Woodcroft 2017-08-03 20:37:25 +10:00
parent a8ead6f91b
commit 92971d68ac
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GPG Key ID: 2A6AD9F4AAC20DF6
1 changed files with 11 additions and 6 deletions
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@ -1636,7 +1636,7 @@ databases.")
(build-system python-build-system) (build-system python-build-system)
(arguments `(#:python ,python-2)) ; only Python 2 is supported (arguments `(#:python ,python-2)) ; only Python 2 is supported
(inputs (inputs
`(("htseq" ,htseq) `(("htseq" ,python2-htseq)
("python-pybedtools" ,python2-pybedtools) ("python-pybedtools" ,python2-pybedtools)
("python-cython" ,python2-cython) ("python-cython" ,python2-cython)
("python-scikit-learn" ,python2-scikit-learn) ("python-scikit-learn" ,python2-scikit-learn)
@ -2981,7 +2981,7 @@ HMMs).")
(define-public htseq (define-public htseq
(package (package
(name "htseq") (name "htseq")
(version "0.6.1") (version "0.9.1")
(source (origin (source (origin
(method url-fetch) (method url-fetch)
(uri (string-append (uri (string-append
@ -2989,14 +2989,16 @@ HMMs).")
version ".tar.gz")) version ".tar.gz"))
(sha256 (sha256
(base32 (base32
"1i85ppf2j2lj12m0x690qq5nn17xxk23pbbx2c83r8ayb5wngzwv")))) "11flgb1381xdhk43bzbfm3vhnszkpqg6jk76rpa5xd1zbrvvlnxg"))))
(build-system python-build-system) (build-system python-build-system)
(arguments `(#:python ,python-2)) ; only Python 2 is supported (native-inputs
`(("python-cython" ,python-cython)))
;; Numpy needs to be propagated when htseq is used as a Python library. ;; Numpy needs to be propagated when htseq is used as a Python library.
(propagated-inputs (propagated-inputs
`(("python-numpy" ,python2-numpy))) `(("python-numpy" ,python-numpy)))
(inputs (inputs
`(("python-pysam" ,python2-pysam))) `(("python-pysam" ,python-pysam)
("python-matplotlib" ,python-matplotlib)))
(home-page "http://www-huber.embl.de/users/anders/HTSeq/") (home-page "http://www-huber.embl.de/users/anders/HTSeq/")
(synopsis "Analysing high-throughput sequencing data with Python") (synopsis "Analysing high-throughput sequencing data with Python")
(description (description
@ -3004,6 +3006,9 @@ HMMs).")
from high-throughput sequencing assays.") from high-throughput sequencing assays.")
(license license:gpl3+))) (license license:gpl3+)))
(define-public python2-htseq
(package-with-python2 htseq))
(define-public java-htsjdk (define-public java-htsjdk
(package (package
(name "java-htsjdk") (name "java-htsjdk")