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| author | Ricardo Wurmus <rekado@elephly.net> | 2022-12-02 19:33:13 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-12-02 21:46:36 +0100 |
| commit | 62da3f9837063b59c615accc86bb80ce03ae301d (patch) | |
| tree | 69f92073c7f33d9d177caa298802b46820e4e467 /gnu | |
| parent | 089b2e4f65fd4ca70e5a089e97e75e825b56efb1 (diff) | |
| download | guix-62da3f9837063b59c615accc86bb80ce03ae301d.tar guix-62da3f9837063b59c615accc86bb80ce03ae301d.tar.gz | |
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.
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 27 |
1 files 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 |