diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 72 |
1 files changed, 43 insertions, 29 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c9d745c0d6..55087ed54a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -21337,32 +21337,35 @@ repeated areas between contigs.") (define-public vembrane (package (name "vembrane") - (version "0.13.2") + (version "1.0.7") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/vembrane/vembrane") - (commit (string-append "v" version)))) + (url "https://github.com/vembrane/vembrane") + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "1gdih56gpqd8ks3sd4ah844kac09hi3g073k9gvazb32ah50900w")))) + "127wmwj0162nfaql68jwxlkz7rbnjya70xrj4j8zwvcnxcj7x5v3")))) (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\""))))))) + #~(modify-phases %standard-phases + (add-after 'unpack 'use-poetry-core + (lambda _ + ;; Patch to use the core poetry API. + (substitute* "pyproject.toml" + (("poetry.masonry.api") "poetry.core.masonry.api"))))))) (inputs - (list python-asttokens python-intervaltree python-numpy - python-pysam python-pyyaml)) + (list python-asttokens + python-intervaltree + python-numpy + python-pysam + python-pyyaml)) (native-inputs - (list poetry python-pytest)) + (list python-poetry-core + python-pytest)) (home-page "https://github.com/vembrane/vembrane") (synopsis "Filter VCF/BCF files with Python expressions") (description "Vembrane simultaneously filters variants based on @@ -24051,24 +24054,35 @@ parser for Python.") (define-public nanosv (package - (name "nanosv") - (version "1.2.4") - (source (origin - (method url-fetch) - (uri (pypi-uri "NanoSV" version)) - (sha256 - (base32 - "1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg")))) - (build-system python-build-system) - (inputs - (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 + (name "nanosv") + (version "1.2.4") + (source + (origin + (method url-fetch) + (uri (pypi-uri "NanoSV" version)) + (sha256 + (base32 "1wl2daj0bwrl8fx5xi8j8hfs3mp3vg3qycy66538n032v1qkc6xg")))) + (build-system pyproject-build-system) + (arguments + (list + #:tests? #f ; No tests upstream, even in git. + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'relax-requirements + (lambda _ + (substitute* "setup.py" + (("'pyvcf'") + "'pyvcf3'"))))))) + (native-inputs (list python-setuptools python-wheel)) + (inputs (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 structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.") - (license license:expat))) + (license license:expat))) (define-public python-strawc (package |