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05/08: gnu: python-pairtools: Update to 1.0.2.
From: |
guix-commits |
Subject: |
05/08: gnu: python-pairtools: Update to 1.0.2. |
Date: |
Fri, 2 Dec 2022 15:48:00 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 62da3f9837063b59c615accc86bb80ce03ae301d
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri Dec 2 19:33:13 2022 +0100
gnu: python-pairtools: Update to 1.0.2.
* gnu/packages/bioinformatics.scm (python-pairtools): Update to 1.0.2.
[source]: Update Github URL.
[arguments]: Update patch in "fix-references" phase.
[native-inputs]: Remove python-nose.
[inputs]: Remove.
[propagated-inputs]: Add python-bioframe, python-pandas, python-pysam,
python-pyyaml, and python-scipy.
[home-page]: Update.
---
gnu/packages/bioinformatics.scm | 27 +++++++++++++++------------
1 file changed, 15 insertions(+), 12 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 560c685d02..09b1910580 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1095,42 +1095,45 @@ e.g. microbiome samples, genomes, metagenomes.")
(define-public python-pairtools
(package
(name "python-pairtools")
- (version "0.3.0")
+ (version "1.0.2")
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/mirnylab/pairtools")
+ (url "https://github.com/open2c/pairtools")
(commit (string-append "v" version))))
(file-name (git-file-name name version))
(sha256
(base32
- "0gr8y13q7sd6yai6df4aavl2470n1f9s3cib6r473z4hr8hcbwmc"))))
+ "0xn4cg4jq3rfn42h8rfwg0k6xkvihjrv32gwldb9y0jp05lzw9cs"))))
(build-system python-build-system)
(arguments
`(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'fix-references
(lambda _
- (substitute* '("pairtools/pairtools_merge.py"
- "pairtools/pairtools_sort.py")
- (("/bin/bash") (which "bash")))
- #t))
+ (substitute* '("pairtools/cli/header.py"
+ "pairtools/cli/merge.py"
+ "pairtools/cli/sort.py")
+ (("/bin/bash") (which "bash")))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(with-directory-excursion "/tmp"
(invoke "pytest" "-v"))))))))
(native-inputs
- (list python-cython python-nose python-pytest))
- (inputs
- `(("python" ,python-wrapper)))
+ (list python-cython python-pytest))
(propagated-inputs
(list htslib ; for bgzip, looked up in PATH
samtools ; looked up in PATH
lz4 ; for lz4c
+ python-bioframe
python-click
- python-numpy))
- (home-page "https://github.com/mirnylab/pairtools")
+ python-numpy
+ python-pandas
+ python-pysam
+ python-pyyaml
+ python-scipy))
+ (home-page "https://github.com/open2c/pairtools")
(synopsis "Process mapped Hi-C data")
(description "Pairtools is a simple and fast command-line framework to
process sequencing data from a Hi-C experiment. Process pair-end sequence
- branch master updated (9ef6286bc3 -> fd44d489b5), guix-commits, 2022/12/02
- 01/08: gnu: python-cellbender: Update to 0.2.2., guix-commits, 2022/12/02
- 04/08: gnu: python-pairtools: Run tests conditionally., guix-commits, 2022/12/02
- 02/08: gnu: python-htsget: Update to 0.2.6., guix-commits, 2022/12/02
- 05/08: gnu: python-pairtools: Update to 1.0.2.,
guix-commits <=
- 03/08: gnu: python-pybedtools: Use pyproject-build-system., guix-commits, 2022/12/02
- 06/08: gnu: Add python-hdmedians., guix-commits, 2022/12/02
- 07/08: gnu: Add python-scikit-bio., guix-commits, 2022/12/02
- 08/08: gnu: python-biom-format: Update to 2.1.12., guix-commits, 2022/12/02