[PATCH] Add seqtk.

[Ben Woodcroft <b.woodcroft@uq.edu.au>]

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I feel somewhat honoured to even be mentioned in the same thread as kseq.h

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From 48d3adae4bcada110df3fb7d8c5ddc55ad2000ff Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
Date: Wed, 24 Jun 2015 15:04:48 +1000
Subject: [PATCH] gnu: Add seqtk.

* gnu/packages/bioinformatics.scm (seqtk): New variable.
---
 gnu/packages/bioinformatics.scm | 45 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8dfaff3..e4575ae 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1573,6 +1573,51 @@ any particular back-end implementation, and supports use of multiple back-ends
 simultaneously.")
     (license license:public-domain)))
 
+(define-public seqtk
+  (let ((commit "4feb6e814"))
+    (package
+      (name "seqtk")
+      ;; version number from running 'seqtk' after installation
+      (version (string-append "1.0-r82." commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/lh3/seqtk.git")
+                      (commit commit)))
+                (sha256
+                 (base32
+                  "0wdkz8chkinfm23cg95nrn797lv12n2wxglwb3s2kvf0iv3rrx01"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f
+	 #:phases
+	 (modify-phases %standard-phases
+	   (delete 'configure)
+	   (replace 'build
+		    (lambda* _
+		      (zero? (system* "make"))))
+	   (replace 'install
+		    (lambda* (#:key outputs #:allow-other-keys)
+		      (let ((bin (string-append
+				  (assoc-ref outputs "out")
+				  "/bin/")))
+			(mkdir-p bin)
+			(copy-file "seqtk" (string-append
+					    bin "seqtk"))
+			(copy-file "trimadap" (string-append
+					    bin "trimadap"))))))))
+      (native-inputs
+       `(("zlib" ,zlib)))
+      (home-page "https://github.com/lh3/seqtk")
+      (synopsis "Toolkit for processing sequences in FASTA/Q formats")
+      (description
+       "Seqtk is a fast and lightweight tool for processing sequences in
+the FASTA or FASTQ format.  It seamlessly parses both FASTA and FASTQ
+files which can also be optionally compressed by gzip.")
+      (license (license:non-copyleft
+		"file://src/LICENSE"
+		"See src/LICENSE in the distribution.")))))
+
 (define-public ngs-java
   (package (inherit ngs-sdk)
     (name "ngs-java")
-- 
2.1.4