diff options
| author | Navid Afkhami <navid.afkhami@mdc-berlin.de> | 2022-12-22 00:16:36 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2022-12-22 00:17:43 +0100 |
| commit | 87c3fab8543396d09be5513aff91c1245aca4229 (patch) | |
| tree | 54e9409cbd4e3916c288693e25ed43d0db360099 /gnu/packages | |
| parent | d07543b8862cecbbc6da69a1f3eda2eb605ccb2e (diff) | |
gnu: Add python-episcanpy.
* gnu/packages/bioinformatics.scm (python-episcanpy): New variable.
Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 56 |
1 files changed, 56 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f80f8b9842..160c44df98 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3689,6 +3689,62 @@ software to answer ad hoc questions.") and random access tool.") (license license:bsd-3))) +(define-public python-episcanpy + (package + (name "python-episcanpy") + (version "0.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "episcanpy" version)) + (sha256 + (base32 + "1qqcyhyzy6idpjmidfdpzwk02hbxm25rymz42h51nlk0vd4r2wwm")))) + (build-system pyproject-build-system) + (arguments + (list + ;; The tests import episcanpy.api, but this is known to not work. + ;; See https://github.com/colomemaria/epiScanpy/issues/133 + #:tests? #false + #:phases + '(modify-phases %standard-phases + ;; 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-anndata + python-bamnostic + python-h5py + python-intervaltree + python-joblib + python-kneed + python-legacy-api-wrap + python-matplotlib + python-natsort + python-networkx + python-numba + python-numpy + python-packaging + python-pandas + python-scanpy + python-scikit-learn + python-scipy + python-seaborn + python-statsmodels + python-tqdm + python-pysam + python-tbb + python-umap-learn)) + (native-inputs (list python-pytest python-setuptools-scm)) + (home-page "https://github.com/colomemaria/epiScanpy") + (synopsis "Tool for epigenomics single cell analysis") + (description + "EpiScanpy is a toolkit to analyse single-cell open +chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) +data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq +analysis tool Scanpy (Genome Biology, 2018).") + (license license:bsd-3))) + (define-public exonerate (package (name "exonerate") |