[med-svn] [subread] 03/04: d/rules: add override_dh_auto_test - run test during build process d/tests/subread-tests: use binaries and test dir from the source package if executed from override_dh_auto_test d/tests/control: Restrictions: allow-stderr d/control: cme fix dpkg-control
Alex Mestiashvili
malex-guest at moszumanska.debian.org
Fri Mar 13 21:11:09 UTC 2015
This is an automated email from the git hooks/post-receive script.
malex-guest pushed a commit to branch master
in repository subread.
commit e583e2dd4ec3449271c9f774222f4113d5146a3e
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date: Fri Mar 13 18:06:18 2015 +0100
d/rules: add override_dh_auto_test - run test during build process
d/tests/subread-tests: use binaries and test dir from the source package
if executed from override_dh_auto_test
d/tests/control: Restrictions: allow-stderr
d/control: cme fix dpkg-control
---
debian/control | 8 +++---
debian/rules | 3 ++
debian/tests/control | 1 +
debian/tests/subread-tests | 71 +++++++++++++++++++++++++++++++---------------
4 files changed, 56 insertions(+), 27 deletions(-)
diff --git a/debian/control b/debian/control
index 59303b2..a82ff3f 100644
--- a/debian/control
+++ b/debian/control
@@ -1,12 +1,12 @@
Source: subread
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>,
+ Andreas Tille <tille at debian.org>
Section: science
Testsuite: autopkgtest
Priority: optional
Build-Depends: debhelper (>= 9),
- zlib1g-dev,
+ zlib1g-dev
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/subread.git
Vcs-Git: git://anonscm.debian.org/debian-med/subread.git
@@ -28,8 +28,8 @@ Depends: ${shlibs:Depends},
${misc:Depends}
Description: data files for subread package
This package provides data files from the original tarball:
- - annotation: Directory including NCBI RefSeq gene annotations for
+ - annotation: Directory including NCBI RefSeq gene annotations for
genomes 'hg19', 'mm10' and 'mm9'. Each row is an exon.
Entrez gene identifiers and chromosomal coordinates are provided for
each exon.
- - test: Directory including test data and scripts.
+ - test: Directory including test data and scripts.
diff --git a/debian/rules b/debian/rules
index 07526d0..468332f 100755
--- a/debian/rules
+++ b/debian/rules
@@ -29,5 +29,8 @@ override_dh_compress:
# do not compress pdfs
dh_compress -X.pdf -Xtest.tar.xz
+override_dh_auto_test:
+ debian/tests/subread-tests $(CURDIR)
+
get-orig-source:
uscan --verbose --force-download --repack --compression xz
diff --git a/debian/tests/control b/debian/tests/control
index 975c40b..3d2992f 100644
--- a/debian/tests/control
+++ b/debian/tests/control
@@ -1 +1,2 @@
Tests: subread-tests
+Restrictions: allow-stderr
diff --git a/debian/tests/subread-tests b/debian/tests/subread-tests
index c23fe96..83c92d1 100755
--- a/debian/tests/subread-tests
+++ b/debian/tests/subread-tests
@@ -1,37 +1,62 @@
#!/bin/sh
+#use test.tar.xz from /usr/share/doc/subread/examples/ if executed with
+#autpkgtest
+#use binaries and test dir from the source package if executed
+#by override_dh_auto_test:
+
set -e
-pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'`
+pkg=subread
tmpdir=$(mktemp -d)
examplesdir=/usr/share/doc/$pkg/examples
-TMPDIR=$(mktemp -d)
-tar -xf $examplesdir/test.tar.xz -C $TMPDIR
-WORKDIR=${TMPDIR}/test
-echo WORKDIR=$WORKDIR
-echo exactSNP test
+if [ $# -eq 0 ]
+then
+ TMPDIR=$(mktemp -d)
+ tar -xf ${examplesdir}/test.tar.xz -C $TMPDIR
+ WORKDIR=${TMPDIR}/test
+else
+ #run tests in the source package if executed during building process
+ TMPDIR=$1
+ cp -r ${TMPDIR}/test ${TMPDIR}/adt_test
+ export PATH=${PATH}:${TMPDIR}/bin:${TMPDIR}:/bin/utilities
+ WORKDIR=${TMPDIR}/adt_test
+fi
+
+
cd $WORKDIR/exactSNP
-exactSNP -g ../chr901.fa -o test-out.VCF -i data/test-in.BAM -b >/dev/null 2>&1
+exactSNP -g ../chr901.fa -o test-out.VCF -i data/test-in.BAM -b
-echo featureCount minimal test
cd $WORKDIR/featureCounts
-featureCounts -a data/test-minimum.GTF -o test-minimum.FC data/test-minimum.sam >/dev/null 2>&1
+featureCounts -a data/test-minimum.GTF -o test-minimum.FC data/test-minimum.sam
-echo subjunc test
cd $WORKDIR/subjunc
mkdir tmp
-subread-buildindex -o tmp/small1 ../chr901.fa >/dev/null 2>&1
-subjunc -i tmp/small1 -o junctions.sam -r data/junction-reads-A.fq -R data/junction-reads-B.fq >/dev/null 2>&1
-subjunc -i tmp/small1 -o junctionsNfusions.bam --BAMoutput -r data/junction-reads-A.fq -R data/junction-reads-B.fq --allJunctions >/dev/null 2>&1
+subread-buildindex -o tmp/small1 ../chr901.fa
+subjunc -i tmp/small1 -o junctions.sam -r data/junction-reads-A.fq \
+-R data/junction-reads-B.fq
+subjunc -i tmp/small1 -o junctionsNfusions.bam --BAMoutput \
+-r data/junction-reads-A.fq -R data/junction-reads-B.fq --allJunctions
-echo subread-align test
cd $WORKDIR/subread-align
mkdir tmp
-subread-buildindex -o tmp/small1 -M100 ../chr901.fa >/dev/null 2>&1
-subread-align -i tmp/small1 -r data/test-noerror-r1.fq -o tmp/test-tmp.sam1 -H -J >/dev/null 2>&1
-subread-align -u -i tmp/small1 -r data/test-noerror-r1.fq -o tmp/test-tmp.sam2 -H -J >/dev/null 2>&1
-subread-align -i tmp/small1 -r data/test-noerror-r1.fq -R data/test-noerror-r2.fq -o tmp/test-tmp.sam3 -H -J >/dev/null 2>&1
-subread-align -u -i tmp/small1 -r data/test-noerror-r1.fq -R data/test-noerror-r2.fq -o tmp/test-tmp.sam4 -Q -J >/dev/null 2>&1
-subread-align -i tmp/small1 -r data/test-error-r1.fq -R data/test-error-r2.fq -o tmp/test-tmp.sam5 -H -J >/dev/null 2>&1
-subread-align -i tmp/small1 --gzFASTQinput -r data/test-err-mut-r1.fq.gz -R data/test-err-mut-r2.fq.gz -o tmp/test-tmp.sam6 -H -J --rg-id MyTestGroup --rg SM:sample1 --rg TP:1 --rg XX:YY >/dev/null 2>&1
-
-rm -rf $TMPDIR
+subread-buildindex -o tmp/small1 -M100 ../chr901.fa
+subread-align -i tmp/small1 -r data/test-noerror-r1.fq \
+ -o tmp/test-tmp.sam1 -H -J
+subread-align -u -i tmp/small1 -r data/test-noerror-r1.fq \
+ -o tmp/test-tmp.sam2 -H -J
+subread-align -i tmp/small1 -r data/test-noerror-r1.fq \
+ -R data/test-noerror-r2.fq -o tmp/test-tmp.sam3 -H -J
+subread-align -u -i tmp/small1 -r data/test-noerror-r1.fq \
+ -R data/test-noerror-r2.fq -o tmp/test-tmp.sam4 -Q -J
+subread-align -i tmp/small1 -r data/test-error-r1.fq \
+ -R data/test-error-r2.fq -o tmp/test-tmp.sam5 -H -J
+subread-align -i tmp/small1 --gzFASTQinput -r data/test-err-mut-r1.fq.gz \
+ -R data/test-err-mut-r2.fq.gz -o tmp/test-tmp.sam6 -H -J \
+ --rg-id MyTestGroup --rg SM:sample1 --rg TP:1 --rg XX:YY
+
+if [ $# -eq 0 ]
+then
+ rm -rf $TMPDIR
+else
+ rm -rf $WORKDIR
+fi
--
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