[med-svn] [velvetoptimiser] 02/11: Package for VelvetOptimiser to complement Velvet, from Bio-Linux
Andreas Tille
tille at debian.org
Fri Sep 22 07:15:25 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository velvetoptimiser.
commit 5f4496e97051607cb687f3b401e8bffa771e2b85
Author: Tim Booth <tbooth at 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 <tbooth at 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 <tbooth at 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 <tbooth at 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.gladman at 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 <tbooth at 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]+
--
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