diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2023-04-24 19:40:15 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-04-24 19:49:04 +0200 |
| commit | bca1496f7290a0ae9a0186f325f3806b6209e6c3 (patch) | |
| tree | 07e0e4ec23b1650e10f8963c98a969a1816c2414 /gnu/packages | |
| parent | 523e5ee2f1c29267f55839d273687e2fd20475d8 (diff) | |
gnu: multiqc: Update to 1.14.
* gnu/packages/bioinformatics.scm (multiqc): Update to 1.14.
[build-system]: Use pyproject-build-system.
[arguments]: Simplify check phase; restore sanity-check phase.
[propagated-inputs]: Add python-rich-click.
[native-inputs]: Update test data.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 22 |
1 files changed, 8 insertions, 14 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d6b8dcaad4..042250e46b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10651,33 +10651,26 @@ replacement for strverscmp.") (define-public multiqc (package (name "multiqc") - (version "1.10.1") + (version "1.14") (source (origin (method url-fetch) (uri (pypi-uri "multiqc" version)) (sha256 (base32 - "0y9sgjca3bp0kk3ngry4zf4q2diyzp5bvzsx5l23nsysfbfkigm4")))) - (build-system python-build-system) + "0qlk2h0765hxp1w9hqf925rh8hq642lzgs6ppg91wln9y02s9fyw")))) + (build-system pyproject-build-system) (arguments `(#:phases (modify-phases %standard-phases (replace 'check - (lambda* (#:key inputs outputs tests? #:allow-other-keys) + (lambda* (#:key inputs tests? #:allow-other-keys) (when tests? (setenv "HOME" "/tmp") (let ((here (getcwd))) (copy-recursively (assoc-ref inputs "tests") "/tmp/tests") - ;; ModuleNotFoundError: No module named 'multiqc.modules.ccs' - (delete-file "/tmp/tests/unit_tests/test_ccs.py") (with-directory-excursion "/tmp/tests" - (setenv "GUIX_PYTHONPATH" - (string-append here ":" (getenv "GUIX_PYTHONPATH"))) - (invoke "python" "-munittest" "discover")))))) - ;; TODO: importing the picard and gatk modules fails for unknown - ;; reasons. - (delete 'sanity-check)))) + (invoke "multiqc" "data" "--ignore" "data/modules"))))))))) (propagated-inputs (list python-click python-coloredlogs @@ -10691,12 +10684,13 @@ replacement for strverscmp.") python-pyyaml python-requests python-rich + python-rich-click python-simplejson python-spectra)) (native-inputs `(("python-pytest" ,python-pytest) ("tests" - ,(let ((commit "02272d48a382beb27489fcf9e6308a0407dc3c2e")) + ,(let ((commit "c3e7400affe3f3ca996973805797af61b93070ba")) (origin (method git-fetch) (uri (git-reference @@ -10705,7 +10699,7 @@ replacement for strverscmp.") (file-name (git-file-name "multiqc-test-data" commit)) (sha256 (base32 - "1bha64wanrigczw4yn81din56396n61j5gqdrkslhslmskcafi91"))))))) + "0wwqbkbfnqj5ax6l0da4csbmv1sw7ya7mwvdwryckaiqmkxy80va"))))))) (home-page "https://multiqc.info") (synopsis "Aggregate bioinformatics analysis reports") (description |