diff options
| author | Navid Afkhami <navid.afkhami@mdc-berlin.de> | 2023-07-23 12:41:46 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-07-31 12:21:12 +0200 |
| commit | c963ba2ebb8097c475ba6e2b5a31be6678f2e74b (patch) | |
| tree | 5766e14d637b1f20f0eaccd1bfe3dcbbe4143f75 /gnu/packages/bioinformatics.scm | |
| parent | fe3e05d8b3dbb255179d3f85aca870e6085bb71a (diff) | |
gnu: Add python-liana-py.
* gnu/packages/bioinformatics.scm (python-liana-py): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 55 |
1 files changed, 55 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 577a0a25b1..6080c899af 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1867,6 +1867,61 @@ protocol. It provides a simple and reliable way to retrieve genomic data from servers supporting the protocol.") (license license:asl2.0))) +(define-public python-liana-py + (package + (name "python-liana-py") + (version "0.1.9") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/saezlab/liana-py") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "00lqrmi38wmdpjlcafgmrnkwsbp0yvm2rya6qs8y6jfizww9ff8i")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + '(list "-k" + ;; These tests require internet access. + (string-append "not test_generate_lr_resource" + " and not test_generate_nondefault_lr_resource")) + #:phases + '(modify-phases %standard-phases + ;; Numba needs a writable directory to cache functions. + (add-before 'build 'set-numba-cache-dir + (lambda _ (setenv "NUMBA_CACHE_DIR" "/tmp")))))) + (propagated-inputs (list python-anndata + python-cell2cell + python-decoupler-py + python-hypothesis + python-ipykernel + python-ipython + python-mofax + python-mudata + python-nbconvert + python-nbsphinx + python-numpydoc + python-omnipath + python-pandas + python-plotnine + python-pypandoc + python-scipy + python-requests + python-scanpy + python-statsmodels + python-tqdm + tzdata)) + (native-inputs + (list python-black python-pytest python-pytest-cov python-numpy)) + (home-page "https://github.com/saezlab/liana-py") + (synopsis "LIANA is a ligand-receptor analysis framework") + (description "This is a Ligand-Receptor inference framework. The +framework enables the use of any LR method with any resources.") + (license license:gpl3+))) + (define-public python-logomaker (package (name "python-logomaker") |