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 <[email protected]> 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 <[email protected]> Uploaders: Alexandre Mestiashvili <[email protected]>, - Andreas Tille <[email protected]>, + Andreas Tille <[email protected]> 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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/subread.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
