[med-svn] [snpomatic] 04/06: add autopkgtest

[Sascha Steinbiss]

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

sascha-guest pushed a commit to branch master
in repository snpomatic.

commit f22f4d4f71a21c76e36b638d0290dee327ae6026
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date:   Mon Mar 7 19:41:23 2016 +0000

    add autopkgtest
---
 debian/changelog          |   1 +
 debian/control            |   1 +
 debian/tests/control      |   3 +
 debian/tests/ref.fasta    | 200 ++++++++++++++++++++++++++++++++++++++++++++++
 debian/tests/test-example |  23 ++++++
 5 files changed, 228 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 7a11c9a..60c8cc6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
 snpomatic (1.0-1) unstable; urgency=medium
 
   * Use upstream versioning scheme.
+  * Add autopkgtest.
 
  -- Sascha Steinbiss <sascha at steinbiss.name>  Mon, 07 Mar 2016 19:21:24 +0000
 
diff --git a/debian/control b/debian/control
index 8c670ac..55a13c4 100644
--- a/debian/control
+++ b/debian/control
@@ -7,6 +7,7 @@ Build-Depends: debhelper (>= 9),
                ruby-ronn,
                antiword
 Standards-Version: 3.9.6
+Testsuite: autopkgtest
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/snpomatic.git
 Vcs-Git: git://anonscm.debian.org/debian-med/snpomatic.git
 Homepage: https://github.com/magnusmanske/snpomatic
diff --git a/debian/tests/control b/debian/tests/control
new file mode 100644
index 0000000..802ef66
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: test-example
+Depends: @, samtools
+Restrictions: allow-stderr
diff --git a/debian/tests/ref.fasta b/debian/tests/ref.fasta
new file mode 100644
index 0000000..e4d5a86
--- /dev/null
+++ b/debian/tests/ref.fasta
@@ -0,0 +1,200 @@
+>ref
+taaccctaaccctaaccctgaccctaaccctaaccctaaccctaaccctaaccagtacac
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+gtcgttggtttcacagcgtcaagccgcgtcggtgtaccaaagaggaggtgacccatcgag
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diff --git a/debian/tests/test-example b/debian/tests/test-example
new file mode 100755
index 0000000..4f9f8cc
--- /dev/null
+++ b/debian/tests/test-example
@@ -0,0 +1,23 @@
+#!/bin/sh
+# autopkgtest check: Run simulated test data through snpomatic
+# Author: Sascha Steinbiss <sascha at steinbiss.name>
+set -e
+
+ORIGDIR=$(pwd)
+DATADIR=$ORIGDIR/debian/tests/
+WORKDIR=$(mktemp -d)
+
+trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM
+cd $WORKDIR
+
+cp $DATADIR/ref.fasta .
+wgsim -N 10000 -r 0.01 -S 42 \
+  ref.fasta \
+  reads.1.fq \
+  reads.2.fq
+findknownsnps --genome=ref.fasta \
+  --fastq=reads.1.fq \
+  --gffout=out.gff \
+  --fastq2=reads.2.fq
+
+[ -s out.gff ]

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git