From 18e0081045703f599aaf1789a206578a2854bdf2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 2 Jun 2021 12:12:00 +0200
Subject: gnu: Add libmaus2.

* gnu/packages/bioinformatics.scm (libmaus2): New variable.
---
 gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 66e790367d..ece59e982e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10969,6 +10969,46 @@ contigs alone.")
     (license (list license:gpl2+        ; bundled ogdf
                    license:gpl3+))))
 
+(define-public libmaus2
+  (package
+    (name "libmaus2")
+    (version "2.0.786")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://gitlab.com/german.tischler/libmaus2")
+                    (commit (string-append version "-release-20210531143054"))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1rxakmwjcx2yq5sjh3v849f7dfw4xzc2fyzf6s28s3p95z84w564"))))
+    (build-system gnu-build-system)
+    ;; The test suite attempts to execute ../test-driver, which does not exist.
+    (arguments '(#:tests? #false))
+    (propagated-inputs
+     `(("zlib" ,zlib)))
+    (native-inputs
+     `(("gcc" ,gcc-10)                   ;Code has C++17 requirements
+       ("pkg-config" ,pkg-config)))
+    (home-page "https://gitlab.com/german.tischler/libmaus2")
+    (synopsis "Collection of data structures and algorithms useful for bioinformatics")
+    (description "libmaus2 is a collection of data structures and
+algorithms.  It contains:
+
+@itemize
+@item I/O classes (single byte and UTF-8);
+@item @code{bitio} classes (input, output and various forms of bit level
+  manipulation);
+@item text indexing classes (suffix and LCP array, fulltext and minute (FM),
+  etc.);
+@item BAM sequence alignment files input/output (simple and collating);
+and many lower level support classes.
+@end itemize\n")
+    ;; The code is explicitly available under the terms of either GPLv2 or
+    ;; GPLv3 according to the AUTHORS file, though most files have a GPLv3+
+    ;; license header.
+    (license (list license:gpl2+ license:gpl3+))))
+
 (define-public r-circus
   (package
     (name "r-circus")
-- 
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