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01/02: gnu: rseqc: Update to 3.0.1.
From: |
guix-commits |
Subject: |
01/02: gnu: rseqc: Update to 3.0.1. |
Date: |
Thu, 27 Feb 2020 11:38:27 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit d24b3b02133e5e3ccc4236656c60377a369bd7b5
Author: Ricardo Wurmus <address@hidden>
AuthorDate: Wed Feb 26 14:19:03 2020 +0100
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.
---
gnu/packages/bioinformatics.scm | 28 +++++++++-------------------
1 file changed, 9 insertions(+), 19 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8ed13b2..51ffa00 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- ;; remove dependency on outdated "distribute" module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