[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.2-42-g6cf23d3

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 96e892657619ade73c8ab21d9b496ca7cd791bff
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Mon Nov 5 10:46:10 2012 +0100

    added autopkgtest framework support
    added a simple bowtie2 test

diff --git a/debian/control b/debian/control
index a8d9d52..26adbad 100644
--- a/debian/control
+++ b/debian/control
@@ -8,6 +8,7 @@ Uploaders: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>,
  Carlos Borroto <carlos.borroto at gmail.com>
 Build-Depends: debhelper (>= 9.0), help2man
 Standards-Version: 3.9.3
+XS-Testsuite: autopkgtest
 Homepage: http://bowtie-bio.sourceforge.net/bowtie2
 Vcs-Browser: http://git.debian.org/?p=debian-med/bowtie2.git
 Vcs-Git: git://git.debian.org/debian-med/bowtie2.git
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..a014edc
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1 @@
+Tests: indexing_ref_genome
diff --git a/debian/tests/indexing_ref_genome b/debian/tests/indexing_ref_genome
new file mode 100755
index 0000000..3d7de12
--- /dev/null
+++ b/debian/tests/indexing_ref_genome
@@ -0,0 +1,9 @@
+#!/bin/sh
+
+set -e
+pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'`
+examplesdir=/usr/share/doc/$pkg/examples
+WORKDIR=$(mktemp -d)
+cd $WORKDIR
+zcat $examplesdir/reference/lambda_virus.fa.gz >lambda_virus.fa
+bowtie2-build lambda_virus.fa lambda_virus >/dev/null 2>&1 

-- 
ultrafast memory-efficient short read aligner