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(python-pyvcf3): New variable, formerly known as "python-pyvcf". --- gnu/packages/bioinformatics.scm | 65 +++++++++++---------------------- 1 file changed, 21 insertions(+), 44 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6f4c5053b6..c593c37d35 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -23715,50 +23715,27 @@ (define-public tombo ;; Some parts may be BSD-3-licensed. (license license:mpl2.0))) -(define-public python-pyvcf - (let ((commit "476169cd457ba0caa6b998b301a4d91e975251d9") - (revision "0")) - (package - (name "python-pyvcf") - (version (git-version "0.6.8" revision commit)) - ;; Use git, because the PyPI tarballs lack test data. - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/jamescasbon/PyVCF.git") - ;; Latest release is not tagged. - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0qf9lwj7r2hjjp4bd4vc7nayrhblfm4qcqs4dbd43a6p4bj2jv5p")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-sample-script - (lambda _ - ;; Add Python 3 compatibility to this sample script. - (substitute* "scripts/vcf_sample_filter.py" - (("print (.*)\n" _ arg) - (string-append "print(" arg ")\n"))))) - (add-after 'install 'remove-installed-tests - ;; Do not install test files. - (lambda* (#:key inputs outputs #:allow-other-keys) - (delete-file-recursively (string-append - (site-packages inputs outputs) - "/vcf/test"))))))) - (native-inputs - ;; Older setuptools is needed for use_2to3. - (list python-cython python-setuptools-57)) - (propagated-inputs - (list python-pysam python-rpy2)) - (home-page "https://github.com/jamescasbon/PyVCF") - (synopsis "Variant Call Format parser for Python") - (description "This package provides a @acronym{VCF,Variant Call Format} +;; This is a fork of the original unmaintained python-pyvcf. +(define-public python-pyvcf3 + (package + (name "python-pyvcf3") + (version "1.0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "PyVCF3" version)) + (sha256 + (base32 "0783pb2p5qx3vgwksc9b9vxbpdq7ax6znff9wa3h80cpicfdf5jb")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-setuptools)) + (native-inputs (list python-setuptools python-wheel)) + (home-page "https://github.com/dridk/PyVCF3") + (synopsis "Variant Call Format parser for Python") + (description "This package provides a @acronym{VCF,Variant Call Format} parser for Python.") - (license license:expat)))) + (license license:expat))) + +(define-deprecated/public-alias python-pyvcf python-pyvcf3) (define-public nanosv (package @@ -23772,7 +23749,7 @@ (define-public nanosv "1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg")))) (build-system python-build-system) (inputs - (list python-configparser python-pysam python-pyvcf)) + (list python-configparser python-pysam python-pyvcf3)) (home-page "https://github.com/mroosmalen/nanosv") (synopsis "Structural variation detection tool for Oxford Nanopore data") (description "NanoSV is a software package that can be used to identify