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commit 5f4496e97051607cb687f3b401e8bffa771e2b85 Author: Tim Booth <tbo...@ceh.ac.uk> Date: Mon Jun 30 09:03:26 2014 +0000 Package for VelvetOptimiser to complement Velvet, from Bio-Linux --- debian/changelog | 13 +++++++++++++ debian/compat | 1 + debian/control | 14 ++++++++++++++ debian/copyright | 28 ++++++++++++++++++++++++++++ debian/docs | 1 + debian/install | 2 ++ debian/patches/no_findbin | 13 +++++++++++++ debian/patches/series | 0 debian/rules | 15 +++++++++++++++ debian/source/format | 1 + debian/watch | 3 +++ 11 files changed, 91 insertions(+) diff --git a/debian/changelog b/debian/changelog new file mode 100644 index 0000000..c775f67 --- /dev/null +++ b/debian/changelog @@ -0,0 +1,13 @@ +velvetoptimiser (2.2.5-1biolinux0.1) trusty; urgency=low + + * Auto-Rebuild for 14.04 + * Add watch file + + -- Tim Booth <tbo...@ceh.ac.uk> Wed, 07 May 2014 18:06:48 +0100 + +velvetoptimiser (2.2.5-0ubuntu1) precise; urgency=low + + * New package + * Remove use of FindBin + + -- Tim Booth <tbo...@ceh.ac.uk> Fri, 23 Aug 2013 11:28:09 +0100 diff --git a/debian/compat b/debian/compat new file mode 100644 index 0000000..45a4fb7 --- /dev/null +++ b/debian/compat @@ -0,0 +1 @@ +8 diff --git a/debian/control b/debian/control new file mode 100644 index 0000000..3899829 --- /dev/null +++ b/debian/control @@ -0,0 +1,14 @@ +Source: velvetoptimiser +Section: science +Priority: extra +Maintainer: Tim Booth <tbo...@ceh.ac.uk> +Build-Depends: debhelper (>= 8), quilt +Standards-Version: 3.9.3 + +Package: velvetoptimiser +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends}, velvet, bioperl (>= 1.4) +Description: Automatically optimise Velvet do novo assembly parameters + VelvetOptimiser is a multi-threaded Perl script for automatically optimising + the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet + de novo sequence assembler. diff --git a/debian/copyright b/debian/copyright new file mode 100644 index 0000000..145a8fd --- /dev/null +++ b/debian/copyright @@ -0,0 +1,28 @@ +Name : VelvetOptimiser +Contact : Simon Gladman, Torsten Seeman +Source : http://www.vicbioinformatics.com/VelvetOptimiser-2.2.5.tar.gz + +Files: * +Copyright: © 2008-2010 Simon Gladman <simon.glad...@monash.edu> +License: GPL-2+ + + VelvetOptimiser is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + VelvetOptimiser is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with Velvet; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + +On Debian systems, the complete text of the GNU General Public +License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. + +Files: debian/* +Copyright: (c) 2013 Tim Booth <tbo...@ceh.ac.uk> +License: GPL-2+ diff --git a/debian/docs b/debian/docs new file mode 100644 index 0000000..e845566 --- /dev/null +++ b/debian/docs @@ -0,0 +1 @@ +README diff --git a/debian/install b/debian/install new file mode 100644 index 0000000..20dd309 --- /dev/null +++ b/debian/install @@ -0,0 +1,2 @@ +VelvetOpt /usr/share/perl5 +velvetoptimiser /usr/bin diff --git a/debian/patches/no_findbin b/debian/patches/no_findbin new file mode 100644 index 0000000..7e024a0 --- /dev/null +++ b/debian/patches/no_findbin @@ -0,0 +1,13 @@ +--- a/VelvetOptimiser.pl ++++ b/VelvetOptimiser.pl +@@ -30,8 +30,8 @@ + # includes + # + use POSIX qw(strftime); +-use FindBin; +-use lib "$FindBin::Bin"; ++#use FindBin; ++#use lib "$FindBin::Bin"; + use threads; + use threads::shared; + use VelvetOpt::Assembly; diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..e69de29 diff --git a/debian/rules b/debian/rules new file mode 100755 index 0000000..5380aec --- /dev/null +++ b/debian/rules @@ -0,0 +1,15 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + + +%: + dh $@ + +override_dh_auto_build: + grep -v FindBin VelvetOptimiser.pl > velvetoptimiser + +override_dh_auto_clean: + rm -f velvetoptimiser diff --git a/debian/source/format b/debian/source/format new file mode 100644 index 0000000..163aaf8 --- /dev/null +++ b/debian/source/format @@ -0,0 +1 @@ +3.0 (quilt) diff --git a/debian/watch b/debian/watch new file mode 100644 index 0000000..90cc245 --- /dev/null +++ b/debian/watch @@ -0,0 +1,3 @@ +version=3 +opts=dversionmangle=s/([~+]dfsg)// \ + http://www.vicbioinformatics.com/software.velvetoptimiser.shtml (?:.*/|)VelvetOptimiser-([0-9.]+).tar.[xgbz2]+ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/velvetoptimiser.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit