From 47839a9ed662f67941bae41a507903280c4f06fd Mon Sep 17 00:00:00 2001
From: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
Date: Sun, 22 Jan 2023 01:49:48 +0100
Subject: gnu: Add python-cmseq.

* gnu/packages/bioinformatics.scm (python-cmseq): New variable.

Co-authored-by: Ricardo Wurmus <rekado@elephly.net>.
---
 gnu/packages/bioinformatics.scm | 38 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 37 insertions(+), 1 deletion(-)

(limited to 'gnu/packages/bioinformatics.scm')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index da65fcb92f..a52a36bdac 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11,7 +11,7 @@
 ;;; Copyright © 2017, 2021, 2022 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
-;;; Copyright © 2018, 2019, 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
+;;; Copyright © 2018-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
 ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com>
 ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org>
@@ -1021,6 +1021,42 @@ Format (GFF) with Biopython integration.")
 from high-throughput single-cell RNA sequencing (scRNA-seq) data.")
     (license license:bsd-3)))
 
+(define-public python-cmseq
+  (package
+    (name "python-cmseq")
+    (version "1.0.4")
+    (source (origin
+              (method url-fetch)
+              (uri (pypi-uri "CMSeq" version))
+              (sha256
+               (base32
+                "0p6a99c299m5wi2z57dgqz52m1z3nfr8mv7kdnk2jvl2p9nql0wk"))))
+    (build-system pyproject-build-system)
+    (arguments
+     (list
+      #:tests? #false ;there are no tests
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'patch-samtools-reference
+           (lambda* (#:key inputs #:allow-other-keys)
+             (substitute* "cmseq/cmseq.py"
+               (("'samtools'")
+                (string-append "'" (search-input-file inputs "/bin/samtools") "'"))))))))
+    (inputs (list samtools))
+    (propagated-inputs
+     (list python-bcbio-gff/biopython-1.73
+           python-biopython-1.73
+           python-numpy
+           python-pandas
+           python-pysam
+           python-scipy))
+    (home-page "https://github.com/SegataLab/cmseq/")
+    (synopsis "Set of utilities on sequences and BAM files")
+    (description
+     "CMSeq is a set of commands to provide an interface to .bam files for coverage
+and sequence consensus.")
+    (license license:expat)))
+
 (define-public python-htsget
   (package
    (name "python-htsget")
-- 
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