From d84bedd830ddc4e108f536ffbe91bd2315e3bd99 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Sat, 9 Jul 2022 10:37:22 +0200
Subject: [PATCH] gnu: Add python-cellbender.
* gnu/packages/bioinformatics.scm (python-cellbender): New variable.
---
gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 525509f56d..325c159df1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -806,6 +806,44 @@ input/output delimiter. When the new functionality is not used, bioawk is
intended to behave exactly the same as the original BWK awk.")
(license license:x11)))
+(define-public python-cellbender
+ (package
+ (name "python-cellbender")
+ (version "0.2.1")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/broadinstitute/CellBender")
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1zav2q8nnss80i25y06fccagkvrqsy7lpylsl4dxv4qkj8p4fnv3"))))
+ (build-system python-build-system)
+ (arguments
+ (list #:tests? #false)) ;there are none
+ (propagated-inputs
+ (list python-anndata
+ python-matplotlib
+ python-numpy
+ python-pandas
+ python-pyro-ppl
+ python-scikit-learn
+ python-scipy
+ python-sphinx
+ python-sphinx-argparse
+ python-sphinx-autodoc-typehints
+ python-sphinx-rtd-theme
+ python-sphinxcontrib-programoutput
+ python-tables))
+ (home-page "https://cellbender.rtfd.io/")
+ (synopsis "Eliminate technical artifacts from single-cell RNA-seq data")
+ (description
+ "CellBender is a software package for eliminating technical artifacts
+from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
+ (license license:bsd-3)))
+
(define-public python-htsget
(package
(name "python-htsget")