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gnu: python-pairtools: Update to 1.0.2.

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* 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.
This commit is contained in:
Ricardo Wurmus 2022-12-02 19:33:13 +01:00
parent 089b2e4f65
commit 62da3f9837
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GPG key ID: 197A5888235FACAC
1 changed files with 15 additions and 12 deletions
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@ -1095,42 +1095,45 @@ (define-public python-biom-format
(define-public python-pairtools (define-public python-pairtools
(package (package
(name "python-pairtools") (name "python-pairtools")
(version "0.3.0") (version "1.0.2")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
(url "https://github.com/mirnylab/pairtools") (url "https://github.com/open2c/pairtools")
(commit (string-append "v" version)))) (commit (string-append "v" version))))
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0gr8y13q7sd6yai6df4aavl2470n1f9s3cib6r473z4hr8hcbwmc")))) "0xn4cg4jq3rfn42h8rfwg0k6xkvihjrv32gwldb9y0jp05lzw9cs"))))
(build-system python-build-system) (build-system python-build-system)
(arguments (arguments
`(#:phases `(#:phases
(modify-phases %standard-phases (modify-phases %standard-phases
(add-after 'unpack 'fix-references (add-after 'unpack 'fix-references
(lambda _ (lambda _
(substitute* '("pairtools/pairtools_merge.py" (substitute* '("pairtools/cli/header.py"
"pairtools/pairtools_sort.py") "pairtools/cli/merge.py"
(("/bin/bash") (which "bash"))) "pairtools/cli/sort.py")
#t)) (("/bin/bash") (which "bash")))))
(replace 'check (replace 'check
(lambda* (#:key tests? #:allow-other-keys) (lambda* (#:key tests? #:allow-other-keys)
(when tests? (when tests?
(with-directory-excursion "/tmp" (with-directory-excursion "/tmp"
(invoke "pytest" "-v")))))))) (invoke "pytest" "-v"))))))))
(native-inputs (native-inputs
(list python-cython python-nose python-pytest)) (list python-cython python-pytest))
(inputs
`(("python" ,python-wrapper)))
(propagated-inputs (propagated-inputs
(list htslib ; for bgzip, looked up in PATH (list htslib ; for bgzip, looked up in PATH
samtools ; looked up in PATH samtools ; looked up in PATH
lz4 ; for lz4c lz4 ; for lz4c
python-bioframe
python-click python-click
python-numpy)) python-numpy
(home-page "https://github.com/mirnylab/pairtools") python-pandas
python-pysam
python-pyyaml
python-scipy))
(home-page "https://github.com/open2c/pairtools")
(synopsis "Process mapped Hi-C data") (synopsis "Process mapped Hi-C data")
(description "Pairtools is a simple and fast command-line framework to (description "Pairtools is a simple and fast command-line framework to
process sequencing data from a Hi-C experiment. Process pair-end sequence process sequencing data from a Hi-C experiment. Process pair-end sequence