From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: [PATCH] Add seqtk. Date: Wed, 24 Jun 2015 15:07:38 +1000 Message-ID: <558A3B1A.4010700@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------000202070002090508090902" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:44538) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z7cua-0002Gy-9F for guix-devel@gnu.org; Wed, 24 Jun 2015 01:07:50 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1Z7cuX-0003qS-3E for guix-devel@gnu.org; Wed, 24 Jun 2015 01:07:48 -0400 Received: from mailhub1.soe.uq.edu.au ([130.102.132.208]:54512 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1Z7cuW-0003qI-Gc for guix-devel@gnu.org; Wed, 24 Jun 2015 01:07:45 -0400 Received: from smtp1.soe.uq.edu.au (smtp1.soe.uq.edu.au [10.138.113.40]) by newmailhub.uq.edu.au (8.14.5/8.14.5) with ESMTP id t5O57eZb021611 for ; Wed, 24 Jun 2015 15:07:40 +1000 Received: from [192.168.1.101] ([103.25.181.216]) (authenticated bits=0) by smtp1.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id t5O57cAe009543 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Wed, 24 Jun 2015 15:07:39 +1000 List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org Sender: guix-devel-bounces+gcggd-guix-devel=m.gmane.org@gnu.org To: "guix-devel@gnu.org" This is a multi-part message in MIME format. --------------000202070002090508090902 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit I feel somewhat honoured to even be mentioned in the same thread as kseq.h --------------000202070002090508090902 Content-Type: text/x-patch; name="0001-gnu-Add-seqtk.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-seqtk.patch" >From 48d3adae4bcada110df3fb7d8c5ddc55ad2000ff Mon Sep 17 00:00:00 2001 From: Ben Woodcroft 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 --------------000202070002090508090902--