diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2022-12-21 13:21:52 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-12-21 23:12:41 +0100 |
| commit | 9e495087d24bcd57937cd79cf373a8bd13e1c240 (patch) | |
| tree | c541732166b51958955ec39fe840a51b4e4b47b5 /gnu/packages | |
| parent | 1194cb1c4030b5c07d05c98f429b73509e524177 (diff) | |
gnu: Add vembrane.
* gnu/packages/bioinformatics.scm (vembrane): New variable.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 38 |
1 files changed, 38 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d8fd2ac3d6..d003822f30 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14443,6 +14443,44 @@ contigs. It then uses paired read information, if available, to retrieve the repeated areas between contigs.") (license license:gpl2+))) +(define-public vembrane + (package + (name "vembrane") + (version "0.13.2") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vembrane/vembrane") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gdih56gpqd8ks3sd4ah844kac09hi3g073k9gvazb32ah50900w")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "pyproject.toml" + (("pysam = \"\\^0.19\"") "pysam = \"^0.20\"") + (("numpy = \\{ version = \"\\^1.23\"") + "numpy = { version = \"^1\""))))))) + (inputs + (list python-asttokens python-intervaltree python-numpy + python-pysam python-pyyaml)) + (native-inputs + (list poetry python-pytest)) + (home-page "https://github.com/vembrane/vembrane") + (synopsis "Filter VCF/BCF files with Python expressions.") + (description "Vembrane allows to simultaneously filter variants based on +any INFO or FORMAT field, CHROM, POS, ID, REF, ALT, QUAL, FILTER, and the +annotation field ANN. When filtering based on ANN, annotation entries are +filtered first. If no annotation entry remains, the entire variant is +deleted.") + (license license:expat))) + (define-public python-velocyto (package (name "python-velocyto") |