From mboxrd@z Thu Jan 1 00:00:00 1970 From: Ben Woodcroft Subject: bug? also [PATCH] Add snap-aligner. Date: Thu, 10 Dec 2015 21:33:42 +1000 Message-ID: <56696316.20402@uq.edu.au> Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="------------070801080204090205090705" Return-path: Received: from eggs.gnu.org ([2001:4830:134:3::10]:60264) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a6zTt-0000OQ-Q1 for guix-devel@gnu.org; Thu, 10 Dec 2015 06:33:54 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1a6zTp-0000Ex-L4 for guix-devel@gnu.org; Thu, 10 Dec 2015 06:33:53 -0500 Received: from mailhub2.soe.uq.edu.au ([130.102.132.209]:44023 helo=newmailhub.uq.edu.au) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1a6zTp-0000Dt-2I for guix-devel@gnu.org; Thu, 10 Dec 2015 06:33:49 -0500 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 tBABXi0w025633 for ; Thu, 10 Dec 2015 21:33:45 +1000 Received: from [192.168.1.105] ([103.25.181.216]) (authenticated bits=0) by smtp1.soe.uq.edu.au (8.14.5/8.14.5) with ESMTP id tBABXhKM056476 (version=TLSv1.2 cipher=DHE-RSA-AES128-SHA bits=128 verify=NOT) for ; Thu, 10 Dec 2015 21:33:44 +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. --------------070801080204090205090705 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Hey, I tried doing the check for reproducibility $ ./pre-inst-env guix build --rounds=3 snap-aligner but it only built once. $ ./pre-inst-env guix build --check snap-aligner ;;; note: source file /home/ben/git/guix/gnu/packages/bioinformatics.scm ;;; newer than compiled /home/ben/git/guix/gnu/packages/bioinformatics.go guix build: error: build failed: unsupported build mode Did I mess that up? Thanks, ben --------------070801080204090205090705 Content-Type: text/x-patch; name="0001-gnu-Add-snap-aligner.patch" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0001-gnu-Add-snap-aligner.patch" >From 6dd854282c75c30b8ae8eb922a2bc65a5be599c0 Mon Sep 17 00:00:00 2001 From: Ben Woodcroft Date: Thu, 10 Dec 2015 20:56:52 +1000 Subject: [PATCH] gnu: Add snap-aligner. * gnu/packages/bioinformatics.scm (snap-aligner): New variable. --- gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 35cec1e..836b4fa 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2792,6 +2792,44 @@ BioPython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.") (license license:gpl3))) +(define-public snap-aligner + (package + (name "snap-aligner") + (version "1.0beta.18") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/amplab/snap/archive/v" + version ".tar.gz")) + (sha256 + (base32 + "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly")) + (file-name (string-append name "-" version ".tar.gz")))) + (build-system gnu-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'check (lambda _ (zero? (system* "./unit_tests")))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin"))) + (mkdir-p bin) + (copy-file "snap-aligner" + (string-append bin "/snap-aligner")) + (copy-file "SNAPCommand" + (string-append bin "/SNAPCommand")))))))) + (native-inputs + `(("zlib" ,zlib))) + (home-page "http://snap.cs.berkeley.edu/") + (synopsis "Short read DNA sequence aligner") + (description + "SNAP is a fast and accurate aligner for short DNA reads. It is +optimized for modern read lengths of 100 bases or higher, and takes advantage +of these reads to align data quickly through a hash-based indexing scheme.") + (license license:asl2.0))) + (define-public star (package (name "star") -- 2.5.0 --------------070801080204090205090705--