diff options
| author | nafkhamdc <navid.afkhami@mdc-berlin.de> | 2024-05-03 09:53:12 +0000 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-05-06 10:37:41 +0200 |
| commit | 00aa6b5a3c1505b033d19c6d3a3021d6d6ecb31b (patch) | |
| tree | 48c45eb4f5f20e3ae816870e462dfea8ee6f2c59 /gnu/packages/bioinformatics.scm | |
| parent | a5fef66b34623622fdaab87c885f7791b860cb97 (diff) | |
gnu: Add python-pyrodigal.
* gnu/packages/bioinformatics.scm (python-pyrodigal): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Change-Id: Iaa0bdb4b918d93f990d5b904f1df3a3f910726b0
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 41 |
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 41e8f07603..3dff39e866 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17852,6 +17852,47 @@ bound.") bgzipped text file that contains a pair of genomic coordinates per line.") (license license:expat))) +(define-public python-pyrodigal + (package + (name "python-pyrodigal") + (version "3.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/althonos/pyrodigal") + (commit (string-append "v" version)) + (recursive? #t))) + (file-name (git-file-name name version)) + (sha256 + (base32 "10vxbm9i33wari0ifsr78xnfn7d0yqwzqpc5pchirjflf1mmnr6w")))) + (build-system pyproject-build-system) + (arguments + (list + #:modules '((ice-9 ftw) + (srfi srfi-1) + (srfi srfi-26) + (guix build utils) + (guix build pyproject-build-system)) + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (let ((cwd (getcwd)) + (libdir (find (cut string-prefix? "lib." <>) + (scandir "build")))) + (with-directory-excursion (string-append cwd "/build/" libdir) + (invoke "python3" "-m" "unittest" "pyrodigal.tests" "-vv"))))))))) + (propagated-inputs (list python-archspec python-importlib-resources)) + (native-inputs (list python-cython-3 python-mock python-unittest2)) + (home-page "https://github.com/althonos/pyrodigal") + (synopsis "Cython bindings and Python interface for Prodigal") + (description + "This package offers Cython bindings and a Python interface for Prodigal. + Prodigal is an ORF finder designed for both genomes and metagenomes.") + (license license:gpl3))) + (define-public python-pyfaidx (package (name "python-pyfaidx") |