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06/06: gnu: Add vembrane.
From: |
guix-commits |
Subject: |
06/06: gnu: Add vembrane. |
Date: |
Wed, 21 Dec 2022 17:14:30 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 9e495087d24bcd57937cd79cf373a8bd13e1c240
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Dec 21 13:21:52 2022 +0100
gnu: Add vembrane.
* gnu/packages/bioinformatics.scm (vembrane): New variable.
---
gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
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")
- branch master updated (fe5836feaf -> 9e495087d2), guix-commits, 2022/12/21
- 05/06: gnu: python-plastid: Update to 0.6.0., guix-commits, 2022/12/21
- 03/06: gnu: htslib: Update to 1.16., guix-commits, 2022/12/21
- 02/06: gnu: pbbam: Use htslib 1.14., guix-commits, 2022/12/21
- 04/06: gnu: python-pysam: Update to 0.20.0., guix-commits, 2022/12/21
- 01/06: gnu: Add htslib-1.14., guix-commits, 2022/12/21
- 06/06: gnu: Add vembrane.,
guix-commits <=