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| author | Ricardo Wurmus <rekado@elephly.net> | 2020-02-26 14:19:03 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2020-02-27 17:38:17 +0100 |
| commit | d24b3b02133e5e3ccc4236656c60377a369bd7b5 (patch) | |
| tree | 4b586923c1d8d8590b6c133e134fa2dbe6498669 /gnu | |
| parent | faa0fa3978bad240f245c79aa487e0594ae9fc9a (diff) | |
| download | patches-d24b3b02133e5e3ccc4236656c60377a369bd7b5.tar patches-d24b3b02133e5e3ccc4236656c60377a369bd7b5.tar.gz | |
gnu: rseqc: Update to 3.0.1.
* 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.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 28 |
1 files changed, 9 insertions, 19 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8ed13b22e5..51ffa00860 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5306,7 +5306,7 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") (define-public rseqc (package (name "rseqc") - (version "2.6.1") + (version "3.0.1") (source (origin (method url-fetch) @@ -5314,28 +5314,18 @@ BAM and Wiggle files in both transcript-coordinate and genomic-coordinate.") (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bundled copy of pysam - (delete-file-recursively "lib/pysam") - (substitute* "setup.py" - ;; remove dependency on outdated "distribute" module - (("^from distribute_setup import use_setuptools") "") - (("^use_setuptools\\(\\)") "") - ;; do not use bundled copy of pysam -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 |