GNU bug report logs - #60124
[PATCH] gnu: Add python-bamnostic.

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From: help-debbugs <at> gnu.org (GNU bug Tracking System)
To: Ricardo Wurmus <rekado <at> elephly.net>
Cc: tracker <at> debbugs.gnu.org
Subject: bug#60124: closed ([PATCH] gnu: Add python-bamnostic.)
Date: Wed, 21 Dec 2022 23:19:02 +0000

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Your message dated Thu, 22 Dec 2022 00:17:49 +0100
with message-id <87zgbgmjli.fsf <at> elephly.net>
and subject line [PATCH] gnu: Add python-bamnostic.
has caused the debbugs.gnu.org bug report #60124,
regarding [PATCH] gnu: Add python-bamnostic.
to be marked as done.

(If you believe you have received this mail in error, please contact
help-debbugs <at> gnu.org.)


-- 
60124: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=60124
GNU Bug Tracking System
Contact help-debbugs <at> gnu.org with problems

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From: Navid Afkhami <navid.afkhami <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Subject: [PATCH] gnu: Add python-bamnostic.
Date: Fri, 16 Dec 2022 17:01:15 +0100

* 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

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From: Ricardo Wurmus <rekado <at> elephly.net>
To: 60124-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: Add python-bamnostic.
Date: Thu, 22 Dec 2022 00:17:49 +0100

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”.

-- 
Ricardo

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