diff mbox series

[bug#60124] gnu: Add python-bamnostic.

Message ID 20221216160115.32252-1-navid.afkhami@mdc-berlin.de
State New
Headers show
Series [bug#60124] gnu: Add python-bamnostic. | expand

Commit Message

nafkhamdc Dec. 16, 2022, 4:01 p.m. UTC 
* gnu/packages/bioinformatics.scm (python-bamnostic): New variable.
---
 gnu/packages/bioinformatics.scm | 72 +++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)

Comments

Ricardo Wurmus Dec. 21, 2022, 11:17 p.m. UTC | #1 
Thanks for the patches!

I split them into two commits, changed the synopses and descriptions,
and moved some inputs around as suggested by “guix lint”.
diff mbox series

Patch

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")