From fd6cd9de8682c7ddf96bf8deb637b1ca6cdbd205 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Wed, 5 Oct 2022 17:59:04 +0200
Subject: gnu: Add megahit.

* gnu/packages/bioinformatics.scm (megahit): New variable.
---
 gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++
 1 file changed, 32 insertions(+)

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

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b467a8b828..becf171880 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -16331,6 +16331,38 @@ (define-public megadepth
 both types of files.")
     (license license:expat)))
 
+(define-public megahit
+  (package
+    (name "megahit")
+    (version "1.2.9")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/voutcn/megahit.git")
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1r5d9nkdmgjsbrpj43q9hy3s8jwsabaz3ji561v18hy47v58923c"))))
+    (build-system cmake-build-system)
+    (arguments
+     (list
+      #:test-target "simple_test"
+      #:phases
+      '(modify-phases %standard-phases
+         (add-after 'unpack 'fix-tests
+           (lambda _
+             (substitute* "src/megahit"
+               (("os.path.join\\(script_path, '..'\\)")
+                "os.path.join(script_path, '../source')")))))))
+    (inputs (list python-wrapper zlib))
+    (home-page "https://www.ncbi.nlm.nih.gov/pubmed/25609793")
+    (synopsis "Meta-genome assembler")
+    (description "Megahit is a fast and memory-efficient NGS assembler.  It is
+optimized for metagenomes, but also works well on generic single genome
+assembly (small or mammalian size) and single-cell assembly.")
+    (license license:gpl3)))
+
 (define-public mudskipper
   (package
     (name "mudskipper")
-- 
cgit v1.2.3