diff options
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 63 |
1 files changed, 63 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 509dc3358b..9ce28596c2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1549,6 +1549,69 @@ from high-throughput single-cell RNA sequencing (scRNA-seq) data.") and sequence consensus.") (license license:expat))) +(define-public python-decoupler-py + ;; This latest commit fixes a bug in test_omnip.py. + (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" + ;; XXX This one fails because the "texts" list + ;; is empty, so there are no texts to adjust. + ;; It is not clear whether this a compatibility + ;; problem with our adjusttext package. + " 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 + "This package provides 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") |