summaryrefslogtreecommitdiff
path: root/gnu/packages/bioinformatics.scm
diff options
context:
space:
mode:
authorRicardo Wurmus <rekado@elephly.net>2020-02-26 14:19:03 +0100
committerRicardo Wurmus <rekado@elephly.net>2020-02-27 17:38:17 +0100
commitd24b3b02133e5e3ccc4236656c60377a369bd7b5 (patch)
tree4b586923c1d8d8590b6c133e134fa2dbe6498669 /gnu/packages/bioinformatics.scm
parentfaa0fa3978bad240f245c79aa487e0594ae9fc9a (diff)
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/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm28
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- ;; remove dependency on outdated "distribute" module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