Author: tbooth-guest
Date: 2014-06-30 09:03:26 +0000 (Mon, 30 Jun 2014)
New Revision: 17342
Added:
trunk/packages/velvetoptimiser/trunk/debian/changelog
trunk/packages/velvetoptimiser/trunk/debian/compat
trunk/packages/velvetoptimiser/trunk/debian/control
trunk/packages/velvetoptimiser/trunk/debian/copyright
trunk/packages/velvetoptimiser/trunk/debian/docs
trunk/packages/velvetoptimiser/trunk/debian/install
trunk/packages/velvetoptimiser/trunk/debian/patches/
trunk/packages/velvetoptimiser/trunk/debian/patches/no_findbin
trunk/packages/velvetoptimiser/trunk/debian/patches/series
trunk/packages/velvetoptimiser/trunk/debian/rules
trunk/packages/velvetoptimiser/trunk/debian/source/
trunk/packages/velvetoptimiser/trunk/debian/source/format
trunk/packages/velvetoptimiser/trunk/debian/watch
Log:
Package for VelvetOptimiser to complement Velvet, from Bio-Linux
Added: trunk/packages/velvetoptimiser/trunk/debian/changelog
===================================================================
--- trunk/packages/velvetoptimiser/trunk/debian/changelog
(rev 0)
+++ trunk/packages/velvetoptimiser/trunk/debian/changelog 2014-06-30
09:03:26 UTC (rev 17342)
@@ -0,0 +1,13 @@
+velvetoptimiser (2.2.5-1biolinux0.1) trusty; urgency=low
+
+ * Auto-Rebuild for 14.04
+ * Add watch file
+
+ -- Tim Booth <[email protected]> Wed, 07 May 2014 18:06:48 +0100
+
+velvetoptimiser (2.2.5-0ubuntu1) precise; urgency=low
+
+ * New package
+ * Remove use of FindBin
+
+ -- Tim Booth <[email protected]> Fri, 23 Aug 2013 11:28:09 +0100
Added: trunk/packages/velvetoptimiser/trunk/debian/compat
===================================================================
--- trunk/packages/velvetoptimiser/trunk/debian/compat
(rev 0)
+++ trunk/packages/velvetoptimiser/trunk/debian/compat 2014-06-30 09:03:26 UTC
(rev 17342)
@@ -0,0 +1 @@
+8
Added: trunk/packages/velvetoptimiser/trunk/debian/control
===================================================================
--- trunk/packages/velvetoptimiser/trunk/debian/control
(rev 0)
+++ trunk/packages/velvetoptimiser/trunk/debian/control 2014-06-30 09:03:26 UTC
(rev 17342)
@@ -0,0 +1,14 @@
+Source: velvetoptimiser
+Section: science
+Priority: extra
+Maintainer: Tim Booth <[email protected]>
+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.
Added: trunk/packages/velvetoptimiser/trunk/debian/copyright
===================================================================
--- trunk/packages/velvetoptimiser/trunk/debian/copyright
(rev 0)
+++ trunk/packages/velvetoptimiser/trunk/debian/copyright 2014-06-30
09:03:26 UTC (rev 17342)
@@ -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 <[email protected]>
+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 <[email protected]>
+License: GPL-2+
Added: trunk/packages/velvetoptimiser/trunk/debian/docs
===================================================================
--- trunk/packages/velvetoptimiser/trunk/debian/docs
(rev 0)
+++ trunk/packages/velvetoptimiser/trunk/debian/docs 2014-06-30 09:03:26 UTC
(rev 17342)
@@ -0,0 +1 @@
+README
Added: trunk/packages/velvetoptimiser/trunk/debian/install
===================================================================
--- trunk/packages/velvetoptimiser/trunk/debian/install
(rev 0)
+++ trunk/packages/velvetoptimiser/trunk/debian/install 2014-06-30 09:03:26 UTC
(rev 17342)
@@ -0,0 +1,2 @@
+VelvetOpt /usr/share/perl5
+velvetoptimiser /usr/bin
Added: trunk/packages/velvetoptimiser/trunk/debian/patches/no_findbin
===================================================================
--- trunk/packages/velvetoptimiser/trunk/debian/patches/no_findbin
(rev 0)
+++ trunk/packages/velvetoptimiser/trunk/debian/patches/no_findbin
2014-06-30 09:03:26 UTC (rev 17342)
@@ -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;
Added: trunk/packages/velvetoptimiser/trunk/debian/patches/series
===================================================================
Added: trunk/packages/velvetoptimiser/trunk/debian/rules
===================================================================
--- trunk/packages/velvetoptimiser/trunk/debian/rules
(rev 0)
+++ trunk/packages/velvetoptimiser/trunk/debian/rules 2014-06-30 09:03:26 UTC
(rev 17342)
@@ -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
Property changes on: trunk/packages/velvetoptimiser/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/velvetoptimiser/trunk/debian/source/format
===================================================================
--- trunk/packages/velvetoptimiser/trunk/debian/source/format
(rev 0)
+++ trunk/packages/velvetoptimiser/trunk/debian/source/format 2014-06-30
09:03:26 UTC (rev 17342)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/velvetoptimiser/trunk/debian/watch
===================================================================
--- trunk/packages/velvetoptimiser/trunk/debian/watch
(rev 0)
+++ trunk/packages/velvetoptimiser/trunk/debian/watch 2014-06-30 09:03:26 UTC
(rev 17342)
@@ -0,0 +1,3 @@
+version=3
+opts=dversionmangle=s/([~+]dfsg)// \
+ http://www.vicbioinformatics.com/software.velvetoptimiser.shtml
(?:.*/|)VelvetOptimiser-([0-9.]+).tar.[xgbz2]+
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