Navid Afkhami wrote 2 years ago
(address . guix-patches@gnu.org)
20221216160115.32252-1-navid.afkhami@mdc-berlin.de
* gnu/packages/bioinformatics.scm (python-bamnostic): New variable.
---
gnu/packages/bioinformatics.scm | 72 +++++++++++++++++++++++++++++++++
1 file changed, 72 insertions(+)
Toggle diff (85 lines)
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