diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 96 |
1 files changed, 62 insertions, 34 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9f0fbd0135..81b46be02f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3333,25 +3333,40 @@ phylogenetic trees also goes by the name simulationmethods for phylogenetic trees, synthetic data generation, or just phylogenetic tree simulation.") (license license:expat))) -;; XXX: Probably unmaintained, build fails with Python 3.11, see -;; <https://github.com/cancerit/parabam/issues/10>. (define-public python-parabam (package (name "python-parabam") - (version "3.0.1") + ;; XXX: Upstream works on modernization of the project, use the latest + ;; commit providing fixes. + ;; See: <https://github.com/cancerit/parabam/issues/10>. + (properties '((commit . "be5bd35012d37df8cfa88771325a0273519c8c98") + (revision . "0"))) + (version (git-version "3.0.1" + (assoc-ref properties 'revision) + (assoc-ref properties 'commit))) (source (origin - (method url-fetch) - (uri (pypi-uri "parabam" version)) + (method git-fetch) + (uri (git-reference + (url "https://github.com/cancerit/parabam") + (commit (assoc-ref properties 'commit)))) + (file-name (git-file-name name version)) (sha256 - (base32 "1cy9q3gzdawi1kilycpd7waymjmrwsg8czwycfp13g301ir9xyp3")) - (modules '((guix build utils))) - (snippet - '(substitute* "setup.py" - (("'argparse',") ""))))) + (base32 "1x0c1zhlfplhm4n07vibvh4jprjsdlypnlig87a8r07d26d4qphh")))) (build-system pyproject-build-system) + (arguments + (list + #:tests? #f ;no tests + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'cythonize + (lambda _ + (with-directory-excursion "parabam" + (for-each (lambda (file) + (invoke "cython" "-3" file "-I" ".")) + (find-files "." ".*\\.pyx$")))))))) (propagated-inputs (list python-numpy python-pysam)) - (native-inputs (list python-setuptools python-wheel)) + (native-inputs (list python-cython python-setuptools)) (home-page "https://github.com/cancerit/parabam") (synopsis "Parallel BAM File Analysis") (description "Parabam is a tool for processing sequencing files in @@ -4571,17 +4586,9 @@ into separate processes; and more.") (base32 "1bv25qhr1dwym2j7llsd3ggnjb9l3h4bchng7bp7cq57s9g0bnjz")))) (build-system pyproject-build-system) - (propagated-inputs - (list python-biopython - python-matplotlib - python-pybio - python-scipy - python-seaborn)) - (native-inputs - (list python-setuptools - python-wheel)) (arguments (list + #:tests? #f ; There are none. #:phases #~(modify-phases %standard-phases (add-before 'check 'set-HOME @@ -4594,6 +4601,14 @@ into separate processes; and more.") (copy-file data-file (string-append data-dir "/" (basename data-file))))))))) + (propagated-inputs + (list python-biopython + python-matplotlib + python-pybio + python-scipy + python-seaborn)) + (native-inputs + (list python-setuptools)) (synopsis "Tool for creating a RNA RBP heatmap in Python") (description "python-scanrbp is a Python package that provides the scanRBP tool that loads RNA-protein binding motif PWM and computes the log-odds scores @@ -4645,9 +4660,7 @@ the scores.") (substitute* "setup.py" ;; bs4 is an alternative name for beautifulsoup4, only used to ;; avoid name squatting on pypi. - (("bs4") "beautifulsoup4") - ;; levenshtein can only be found as python-levenshtein - (("levenshtein") "python-levenshtein")))) + (("bs4") "beautifulsoup4")))) ;; fireducks seems to be a binary-only python-panda replacement (add-after 'unpack 'remove-fireducks (lambda _ @@ -4895,7 +4908,10 @@ consensus sequences.") (("'argparse[^']*',") "") ;only for python2 (("==") - ">=")))) + ">=") + ;; This package changed names. + (("python-Levenshtein") + "levenshtein")))) (add-before 'build 'build-libssw (lambda _ (with-directory-excursion "libs/striped_smith_waterman" @@ -8133,17 +8149,29 @@ exploration.") (define-public python-illumina-utils (package (name "python-illumina-utils") - (version "2.12") - (source (origin - (method url-fetch) - (uri (pypi-uri "illumina-utils" version)) - (sha256 - (base32 - "0z9g0prj7pmgl5z4vdpxv3v30grzhc194801qnf0wqzgy7w3aj2s")))) + (version "2.13") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/meren/illumina-utils") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "15cyb5slw07va5siq8nzc0nwcgnvx1hmqqrgwk2v0fxy250fp9v4")))) (build-system pyproject-build-system) - (arguments (list #:tests? #false)) ;there are none - (propagated-inputs (list python-matplotlib python-numpy python-levenshtein)) - (native-inputs (list python-setuptools python-wheel python-pip)) + (arguments + (list + #:tests? #f ;there are none + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-requirements + (lambda _ + (substitute* "requirements.txt" + (("python-Levenshtein") + "levenshtein"))))))) + (propagated-inputs (list python-levenshtein python-matplotlib python-numpy)) + (native-inputs (list python-pip python-setuptools)) (home-page "https://github.com/meren/illumina-utils") (synopsis "Library and scripts to work with Illumina paired-end data") (description |