I feel somewhat honoured to even be mentioned in the same thread as kseq.h
>From 48d3adae4bcada110df3fb7d8c5ddc55ad2000ff Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <[email protected]>
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
