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dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=JRfmebtx; 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"; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none) X-Migadu-Scanner: scn1.migadu.com X-TUID: EPa8QGa9uLIw * gnu/packages/bioinformatics.scm (python-bamnostic): New variable. --- gnu/packages/bioinformatics.scm | 72 +++++++++++++++++++++++++++++++++ 1 file changed, 72 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e8da00d805..cb423312a8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3646,6 +3646,78 @@ (define-public edirect-go-programs go-golang-org-x-image go-golang-org-x-text)))) +(define-public python-bamnostic + (package + (name "python-bamnostic") + (version "1.1.8") + (source (origin + (method url-fetch) + (uri (pypi-uri "bamnostic" version)) + (sha256 + (base32 + "0cjpzyqz6r4lmiwry2gcxdczwpkhl3lyyjg4s8addln17691ysxk")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-pytest)) + (home-page "https://github.com/betteridiot/bamnostic/") + (synopsis + "A tool for binary alignment map, random access and parsing") + (description + "A tool for binary alignment map, random access and parsing.") + (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 + #:tests? #f + #: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-setuptools-scm + python-statsmodels + python-tqdm + python-pysam + python-pytest + python-tbb + python-umap-learn)) + (native-inputs (list python-pytest)) + (home-page "http://github.com/colomemaria/epiScanpy") + (synopsis "A tool for epigenomics single cell analysis") + (description + "A toolkit to analyse single-cell open chromatin +and single-cell DNA methylation data.") + (license license:bsd-3))) + (define-public exonerate (package (name "exonerate") -- 2.34.1