[med-svn] [subread] 01/05: d/control: add autopkgtest d/rules: add get-orig-source rule d/tests/control: tests d/tests/exactSNP: tests

[Alex Mestiashvili]

This is an automated email from the git hooks/post-receive script.

malex-guest pushed a commit to branch master
in repository subread.

commit 858a073fc9b00ddffbafb5784da898cdbc1a3610
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed Mar 11 11:09:49 2015 +0100

     d/control: add  autopkgtest
     d/rules: add get-orig-source rule
     d/tests/control: tests
     d/tests/exactSNP: tests
---
 debian/control        |  5 ++++-
 debian/rules          |  3 +++
 debian/tests/control  |  2 ++
 debian/tests/exactSNP | 20 ++++++++++++++++++++
 4 files changed, 29 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 0da9d85..59303b2 100644
--- a/debian/control
+++ b/debian/control
@@ -1,6 +1,9 @@
 Source: subread
-Maintainer: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>,
+           Andreas Tille <tille at debian.org>,
 Section: science
+Testsuite: autopkgtest
 Priority: optional
 Build-Depends: debhelper (>= 9),
                zlib1g-dev,
diff --git a/debian/rules b/debian/rules
index 251df4b..8316e64 100755
--- a/debian/rules
+++ b/debian/rules
@@ -25,3 +25,6 @@ override_dh_auto_install:
 override_dh_compress:
 # do not compress pdfs
 	dh_compress -a -X.pdf
+
+get-orig-source:
+	uscan --verbose --force-download --repack --compression xz
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..4b83b61
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,2 @@
+Tests: exactSNP
+Depends: subread-data
diff --git a/debian/tests/exactSNP b/debian/tests/exactSNP
new file mode 100755
index 0000000..4f39039
--- /dev/null
+++ b/debian/tests/exactSNP
@@ -0,0 +1,20 @@
+#!/bin/sh
+
+set -e
+pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'`
+testdir=../../test/
+bindir=../$(pkg)/bin/
+ls -l ../$(pkg)
+CURDIR=`pwd`
+echo CURDIR=$CURDIR
+WORKDIR=$(mktemp -d)
+cd $WORKDIR
+
+#for file in test/chr901.fa.gz test/exactSNP/data/test-in.BAM.gz
+#do      
+#        extracted=`echo $file | awk -F/ '{print $NF}'`
+#        zcat $examplesdir/$file >${extracted%.gz}
+#done
+#cd -
+
+$bindir/exactSNP -g $testdir/chr901.fa -o test-out.VCF -i $testdir/test-in.BAM -b >/dev/null 2>&1

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