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[propagated-inputs]: Add r-yaml, r-rsamtools, r-biocmanager, r-here, r-genomicranges, r-readr, r-tidyr, r-stringr, r-optparse, r-openxlsx, r-dplyr, and r-upsetr. Change-Id: I8c1bb556048b406b95e081155a46da17a6be5676 --- gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++-------------- 1 file changed, 43 insertions(+), 33 deletions(-) base-commit: c0895371c5759c7d9edb330774e90f192cc4cf2c diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a47e84bc33..66d1a21ffe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5130,47 +5130,57 @@ (define-public python-baltica (package (name "python-baltica") (version "1.1.2") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/dieterich-lab/Baltica") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r")))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/dieterich-lab/Baltica") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "001ac03v9pbqqzf9pv7v8gf0296ksa4f0v3wdmpa6m9701skqi4r")))) (build-system pyproject-build-system) (arguments (list - #:phases - '(modify-phases %standard-phases - (replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - ;; The tests need to be run from elsewhere... - (mkdir-p "/tmp/test") - (copy-recursively ".tests" "/tmp/test") - (with-directory-excursion "/tmp/test" - (invoke "pytest" "-v" "--doctest-modules")))))))) - (propagated-inputs - (list gunicorn - python-anndata - python-click - python-flask - python-flask-wtf - python-h5py - python-numpy - python-psutil - python-pysam - python-pyyaml - python-scipy - snakemake-7)) + #:phases '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; The tests need to be run from elsewhere... + (mkdir-p "/tmp/test") + (copy-recursively ".tests" "/tmp/test") + (with-directory-excursion "/tmp/test" + (invoke "pytest" "-v" "--doctest-modules")))))))) + (propagated-inputs (list gunicorn + python-anndata + python-click + python-flask + python-flask-wtf + python-h5py + python-numpy + python-psutil + python-pysam + python-pyyaml + python-scipy + r-yaml + r-rsamtools + r-biocmanager + r-here + r-genomicranges + r-readr + r-tidyr + r-stringr + r-optparse + r-openxlsx + r-dplyr + r-upsetr + snakemake-7)) (native-inputs (list python-cython python-pyfakefs python-pytest)) (home-page "https://github.com/dieterich-lab/Baltica") (synopsis "Integrated splice junction usage analysis") (description "This framework facilitates the execution of @dfn{differential junction -usage} (DJU) methods. Additionally, it enables the integration of results from +usage} (DJU) methods. Additionally, it enables the integration of results from multiple DJU methods.") (license license:expat)))