diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 64 |
1 files changed, 40 insertions, 24 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2c1f0e7493..788e7ae836 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8414,41 +8414,57 @@ replacement for strverscmp.") (define-public multiqc (package (name "multiqc") - (version "1.5") + (version "1.10.1") (source (origin (method url-fetch) (uri (pypi-uri "multiqc" version)) (sha256 (base32 - "02iihfl0w0hpnr4pa0sbd1y9qxrg3ycyhjp5lidkcrqh1lmzs3zy")))) + "0y9sgjca3bp0kk3ngry4zf4q2diyzp5bvzsx5l23nsysfbfkigm4")))) (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key inputs outputs 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 "PYTHONPATH" (string-append here ":" (getenv "PYTHONPATH"))) + (invoke "python" "-munittest" "discover"))))))))) (propagated-inputs - `(("python-jinja2" ,python-jinja2) - ("python-simplejson" ,python-simplejson) - ("python-pyyaml" ,python-pyyaml) - ("python-click" ,python-click) - ("python-spectra" ,python-spectra) - ("python-requests" ,python-requests) - ("python-markdown" ,python-markdown) + `(("python-click" ,python-click) + ("python-coloredlogs" ,python-coloredlogs) + ("python-future" ,python-future) + ("python-jinja2" ,python-jinja2) ("python-lzstring" ,python-lzstring) + ("python-markdown" ,python-markdown) ("python-matplotlib" ,python-matplotlib) + ("python-networkx" ,python-networkx) ("python-numpy" ,python-numpy) - ;; MultQC checks for the presence of nose at runtime. - ("python-nose" ,python-nose))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'relax-requirements - (lambda _ - (substitute* "setup.py" - ;; MultiQC 1.5 ‘requires’ a version of python-matplotlib older - ;; than the one in Guix, but should work fine with 2.2.2. - ;; See <https://github.com/ewels/MultiQC/issues/725> and - ;; <https://github.com/ewels/MultiQC/issues/732> for details. - (("['\"]matplotlib.*?['\"]") - "'matplotlib'")) - #t))))) + ("python-pyyaml" ,python-pyyaml) + ("python-requests" ,python-requests) + ("python-rich" ,python-rich) + ("python-simplejson" ,python-simplejson) + ("python-spectra" ,python-spectra))) + (native-inputs + `(("python-pytest" ,python-pytest) + ("tests" + ,(let ((commit "02272d48a382beb27489fcf9e6308a0407dc3c2e")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ewels/MultiQC_TestData") + (commit commit))) + (file-name (git-file-name "multiqc-test-data" commit)) + (sha256 + (base32 + "1bha64wanrigczw4yn81din56396n61j5gqdrkslhslmskcafi91"))))))) (home-page "https://multiqc.info") (synopsis "Aggregate bioinformatics analysis reports") (description |