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dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=RTQzKVhl; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 415A6DF67 X-Spam-Score: 0.31 X-TUID: fhIQZFHeqVex * gnu/packages/bioinformatics.scm (python-decoupler-py): New variable. --- gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++ 1 file changed, 58 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 509dc3358b..12455984ed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1549,6 +1549,64 @@ (define-public python-cmseq and sequence consensus.") (license license:expat))) +(define-public python-decoupler-py + ;; This latest commit fixes the bug in test_omnip.py file. check_if_omnipath() has changed to _check_if_omnipath() + (let ((commit "b84c524ec4a9280a56c0db963e2c7b010316ce8f") + (revision "1")) + (package + (name "python-decoupler-py") + (version (git-version "1.3.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/decoupler-py") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0d74yr5jqc52vcxaca84kxqw7m5rbazpmvnrcp2y4xxrj6yr1sfc")))) + (build-system pyproject-build-system) + (arguments + (list #:test-flags '(list "-k" + ;; These tests require internet access + (string-append "not test_get_resource" + " and not test_show_resources" + " and not test_get_dorothea" + " and not test_get_progeny" + " and not test_plot_volcano")) + #:phases '(modify-phases %standard-phases + (add-before 'check 'set-home + ;; Some tests require a home directory to be set. + (lambda _ + (setenv "HOME" "/tmp"))) + ;; Numba needs a writable dir to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ + (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-adjusttext + python-anndata + python-ipython + python-matplotlib + python-nbsphinx + python-numba + python-numpy + python-numpydoc + python-omnipath + python-scanpy + python-scikit-learn + python-scipy + python-skranger + python-tqdm + python-typing-extensions)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/saezlab/decoupler-py") + (synopsis + "Framework for modeling, analyzing and interpreting single-cell RNA-seq data") + (description + "Different statistical methods to extract biological activities +from omics data within a unified framework.") + (license license:gpl3+)))) + (define-public python-demuxem (package (name "python-demuxem") base-commit: 9ad8b0c2ef10d8de01bad25f54337c5df35aa842 -- 2.34.1