[med-svn] [SCM] abyss branch, master, updated. upstream/1.3.3-2-ge3662b6

[Andreas Tille]

The following commit has been merged in the master branch:
commit e3662b68f68e4bf06b3ca764bdeae83b185a62e9
Author: Andreas Tille <tille at debian.org>
Date:   Sun Apr 1 08:34:41 2012 +0200

    Inject current state of packaging

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..176feb0
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,45 @@
+abyss (1.3.3-1) unstable; urgency=low
+
+  * New upstream release.
+  * Some components are dual-licensed BCCA-Academic or GPL-3+.
+  * Bump Standards-Version to 3.9.3.
+
+ -- Shaun Jackman <sjackman at debian.org>  Tue, 13 Mar 2012 15:43:49 -0700
+
+abyss (1.3.2-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org>  Tue, 13 Dec 2011 17:04:24 -0800
+
+abyss (1.3.1-1) unstable; urgency=low
+
+  * New upstream release.
+
+ -- Shaun Jackman <sjackman at debian.org>  Mon, 24 Oct 2011 11:32:59 -0700
+
+abyss (1.3.0-1) unstable; urgency=low
+
+  * New upstream release.
+  * Add libboost-graph-dev to Build-Depends.
+
+ -- Shaun Jackman <sjackman at debian.org>  Sun, 11 Sep 2011 10:00:13 -0700
+
+abyss (1.2.7-3) unstable; urgency=low
+
+  * Align/Aligner.cpp, Scaffold/scaffold.cc: Fix FTBFS bug for GCC 4.6.
+
+ -- Shaun Jackman <sjackman at debian.org>  Mon, 15 Aug 2011 11:07:19 -0700
+
+abyss (1.2.7-2) unstable; urgency=low
+
+  * debian/control: Add `XS-Autobuild: yes'. Suggest openmpi-bin.
+  * debian/copyright: Change `Format-Specification' to `Format'.
+
+ -- Shaun Jackman <sjackman at debian.org>  Thu, 21 Jul 2011 09:55:52 -0700
+
+abyss (1.2.7-1) unstable; urgency=low
+
+  * Initial release. Closes: #631534.
+
+ -- Shaun Jackman <sjackman at debian.org>  Fri, 24 Jun 2011 12:16:36 -0700
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..7f8f011
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+7
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..01069bd
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,24 @@
+Source: abyss
+Section: non-free/science
+Priority: optional
+Maintainer: Shaun Jackman <sjackman at debian.org>
+Build-Depends: debhelper (>= 7.0.50~), autotools-dev,
+ libboost-graph-dev, libopenmpi-dev, libsparsehash-dev
+Standards-Version: 3.9.3
+Homepage: http://www.bcgsc.ca/platform/bioinfo/software/abyss
+XS-Autobuild: yes
+
+Package: abyss
+Architecture: any
+Depends: make, ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
+Suggests: openmpi-bin
+Description: de novo, parallel, sequence assembler for short reads
+ ABySS is a de novo, parallel, sequence assembler that is designed for
+ short reads. It may be used to assemble genome or transcriptome
+ sequence data. Parallelization is achieved using MPI, OpenMP and
+ pthread.
+ .
+ To cite your use of ABySS, please reference
+ ABySS: A parallel assembler for short read sequence data. Simpson JT,
+ Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Genome Research,
+ 2009-June.
diff --git a/COPYRIGHT b/debian/copyright
similarity index 100%
copy from COPYRIGHT
copy to debian/copyright
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..fd37f09
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,4 @@
+README
+README.css
+README.html
+doc/flowchart.pdf
diff --git a/debian/install b/debian/install
new file mode 100644
index 0000000..b23400c
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+usr/bin/abyss-pe usr/bin
+usr/bin/* usr/lib/abyss
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..43e261f
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+doc/*.1
diff --git a/debian/patches/abyss-pe b/debian/patches/abyss-pe
new file mode 100644
index 0000000..1e90fa1
--- /dev/null
+++ b/debian/patches/abyss-pe
@@ -0,0 +1,11 @@
+--- abyss-1.3.3.orig/bin/abyss-pe	2012-03-13 16:24:07.000000000 -0700
++++ abyss-1.3.3/bin/abyss-pe	2012-03-13 16:24:46.000000000 -0700
+@@ -2,6 +2,8 @@
+ # Run the ABySS assembler.
+ # Written by Shaun Jackman <sjackman at bcgsc.ca>.
+ 
++PATH:=/usr/lib/abyss:${PATH}
++
+ # Set pipefail to require that all commands of a pipe must succeed.
+ SHELL=/bin/bash -o pipefail
+ 
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..f09fd48
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+abyss-pe
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..a14fb9c
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,12 @@
+#!/usr/bin/make -f
+
+export DH_OPTIONS
+
+%:
+	dh  $@
+
+override_dh_auto_configure:
+	dh_auto_configure -- --with-mpi=/usr/lib/openmpi
+
+override_dh_auto_install:
+	dh_auto_install --destdir=debian/tmp
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..9cfe345
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://www.bcgsc.ca/downloads/abyss/ abyss-(.+)\.tar\.gz

-- 
Packaging of abyss in Debian