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envelope-from=Navid.Afkhami@mdc-berlin.de; helo=b2062.mx.srv.dfn.de X-Spam_score_int: -43 X-Spam_score: -4.4 X-Spam_bar: ---- X-Spam_report: (-4.4 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_MED=-2.3, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001, T_SCC_BODY_TEXT_LINE=-0.01 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioinformatics.scm (python-baltica): New variable. --- gnu/packages/bioinformatics.scm | 43 +++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) base-commit: 34b56974dfe720e5e30f04409ac216747d7e3f5c diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6080c899af..6d745262b3 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5056,6 +5056,49 @@ (define-public edirect-go-programs go-golang-org-x-image go-golang-org-x-text)))) +(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")))) + (build-system pyproject-build-system) + (arguments + (list #:phases '(modify-phases %standard-phases + (replace 'check + (lambda _ + ;; 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 python-anndata + python-click + python-flask + python-flask-wtf + gunicorn + python-h5py + python-pysam + python-numpy + python-psutil + python-pyyaml + python-scipy + snakemake-7)) + (native-inputs (list python-pytest python-pyfakefs python-cython)) + (home-page "https://github.com/dieterich-lab/Baltica") + (synopsis "Integrated splice junction usage analysis") + (description + "This framework facilitates the execution of differential junction usage methods. +Additionally, it enables the integration of results from multiple DJU methods.") + (license license:expat))) + (define-public python-bamnostic (package (name "python-bamnostic")