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gnu: rseqc: Update to 3.0.1.

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* gnu/packages/bioinformatics.scm (rseqc): Update to 3.0.1.
[source]: Remove snippet.
[arguments]: Remove to build with Python 3.
[inputs]: Replace python2-cython, python2-pysam, and python2-numpy with
python-cython, python-pysam, and python-numpy, respectively; add
python-bx-python and python-pybigwig.
[native-inputs]: Replace python2-nose with python-nose.
This commit is contained in:
Ricardo Wurmus 2020-02-26 14:19:03 +01:00
parent faa0fa3978
commit d24b3b0213
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GPG key ID: 197A5888235FACAC
1 changed files with 9 additions and 19 deletions
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28
gnu/packages/bioinformatics.scm
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@ -5306,7 +5306,7 @@ (define-public rsem
(define-public rseqc
(package
(name "rseqc")
(version "2.6.1")
(version "3.0.1")
(source
(origin
(method url-fetch)
@ -5314,28 +5314,18 @@ (define-public rseqc
(string-append "mirror://sourceforge/rseqc/"
"RSeQC-" version ".tar.gz"))
(sha256
(base32 "15ly0254yi032qzkdplg00q144qfdsd986gh62829rl5bkxhj330"))
(modules '((guix build utils)))
(snippet
'(begin
;; remove bundled copy of pysam
(delete-file-recursively "lib/pysam")
(substitute* "setup.py"
;; remove dependency on outdated "distribute" module
(("^from distribute_setup import use_setuptools") "")
(("^use_setuptools\\(\\)") "")
;; do not use bundled copy of pysam
(("^have_pysam = False") "have_pysam = True"))
#t))))
(base32
"0gbb9iyb7swiv5455fm5rg98r7l6qn27v564yllqjd574hncpx6m"))))
(build-system python-build-system)
(arguments `(#:python ,python-2))
(inputs
`(("python-cython" ,python2-cython)
("python-pysam" ,python2-pysam)
("python-numpy" ,python2-numpy)
`(("python-cython" ,python-cython)
("python-bx-python" ,python-bx-python)
("python-pybigwig" ,python-pybigwig)
("python-pysam" ,python-pysam)
("python-numpy" ,python-numpy)
("zlib" ,zlib)))
(native-inputs
`(("python-nose" ,python2-nose)))
`(("python-nose" ,python-nose)))
(home-page "http://rseqc.sourceforge.net/")
(synopsis "RNA-seq quality control package")
(description