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commit 5114b44996ad89f7ac18126363c584097d3516a8 Author: Alexandre Mestiashvili <[email protected]> Date: Fri Mar 13 15:50:23 2015 +0100 d/rules: override_dh_installexamples - install compressed test dir d/tests: substitute tests with one doing multiple tests, remove single tests --- debian/rules | 5 ++++- debian/subread-data.install | 1 - debian/tests/control | 8 +------- debian/tests/exactSNP | 16 ---------------- debian/tests/fc-minimal | 7 ------- debian/tests/subjunc | 9 --------- debian/tests/subread-align | 13 ------------- debian/tests/subread-tests | 37 +++++++++++++++++++++++++++++++++++++ 8 files changed, 42 insertions(+), 54 deletions(-) diff --git a/debian/rules b/debian/rules index 8316e64..07526d0 100755 --- a/debian/rules +++ b/debian/rules @@ -22,9 +22,12 @@ override_dh_auto_install: find $(CURDIR) -name "*.gz" -exec bash -c 'name="{}"; gzip -d "{}"; gzip -n "$${name%.*}"' \; dh_auto_install +override_dh_installexamples: + tar -cJf $(CURDIR)/debian/subread-data/usr/share/doc/subread/examples/test.tar.xz test/ + override_dh_compress: # do not compress pdfs - dh_compress -a -X.pdf + dh_compress -X.pdf -Xtest.tar.xz get-orig-source: uscan --verbose --force-download --repack --compression xz diff --git a/debian/subread-data.install b/debian/subread-data.install index 10b1661..ae2db19 100644 --- a/debian/subread-data.install +++ b/debian/subread-data.install @@ -1,2 +1 @@ annotation usr/share/doc/subread/examples -test usr/share/doc/subread/examples diff --git a/debian/tests/control b/debian/tests/control index 415f1e5..975c40b 100644 --- a/debian/tests/control +++ b/debian/tests/control @@ -1,7 +1 @@ -Tests: exactSNP - -Tests: fc-minimal - -Tests: subjunc - -Tests: subread-align +Tests: subread-tests diff --git a/debian/tests/exactSNP b/debian/tests/exactSNP deleted file mode 100755 index 52f6177..0000000 --- a/debian/tests/exactSNP +++ /dev/null @@ -1,16 +0,0 @@ -#!/bin/sh - -set -e -pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'` -tmpdir=$(mktemp -d) -examplesdir=/usr/share/doc/$pkg/examples/test -WORKDIR=$(mktemp -d) -cd $WORKDIR -for file in chr901.fa.gz exactSNP/data/test-in.BAM.gz -do - extracted=`echo $file | awk -F/ '{print $NF}'` - zcat $examplesdir/$file >${extracted%.gz} -done - - -exactSNP -g chr901.fa -o $tmpdir/test-out.VCF -i test-in.BAM -b >/dev/null 2>&1 diff --git a/debian/tests/fc-minimal b/debian/tests/fc-minimal deleted file mode 100755 index f57006c..0000000 --- a/debian/tests/fc-minimal +++ /dev/null @@ -1,7 +0,0 @@ -#!/bin/sh - -set -e -workdir=test/featureCounts -cd $workdir -tmpdir=$(mktemp -d) -featureCounts -a data/test-minimum.GTF -o $tmpdir/test-minimum.FC data/test-minimum.sam >/dev/null 2>&1 diff --git a/debian/tests/subjunc b/debian/tests/subjunc deleted file mode 100755 index 9bdf7cf..0000000 --- a/debian/tests/subjunc +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/sh - -set -e -workdir=test/subjunc -cd $workdir -tmpdir=$(mktemp -d) -subread-buildindex -o $tmpdir/small1 ../chr901.fa >/dev/null 2>&1 -subjunc -i $tmpdir/small1 -o $tmpdir/junctions.sam -r data/junction-reads-A.fq -R data/junction-reads-B.fq >/dev/null 2>&1 -subjunc -i $tmpdir/small1 -o $tmpdir/junctionsNfusions.bam --BAMoutput -r data/junction-reads-A.fq -R data/junction-reads-B.fq --allJunctions >/dev/null 2>&1 diff --git a/debian/tests/subread-align b/debian/tests/subread-align deleted file mode 100755 index 3f1a904..0000000 --- a/debian/tests/subread-align +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/sh - -set -e -workdir=test/subread-align -cd $workdir -tmpdir=$(mktemp -d) -subread-buildindex -o $tmpdir/small1 -M100 ../chr901.fa >/dev/null 2>&1 -subread-align -i $tmpdir/small1 -r data/test-noerror-r1.fq -o $tmpdir/test-tmp.sam1 -H -J >/dev/null 2>&1 -subread-align -u -i $tmpdir/small1 -r data/test-noerror-r1.fq -o $tmpdir/test-tmp.sam2 -H -J >/dev/null 2>&1 -subread-align -i $tmpdir/small1 -r data/test-noerror-r1.fq -R data/test-noerror-r2.fq -o $tmpdir/test-tmp.sam3 -H -J >/dev/null 2>&1 -subread-align -u -i $tmpdir/small1 -r data/test-noerror-r1.fq -R data/test-noerror-r2.fq -o $tmpdir/test-tmp.sam4 -Q -J >/dev/null 2>&1 -subread-align -i $tmpdir/small1 -r data/test-error-r1.fq -R data/test-error-r2.fq -o $tmpdir/test-tmp.sam5 -H -J >/dev/null 2>&1 -subread-align -i $tmpdir/small1 --gzFASTQinput -r data/test-err-mut-r1.fq.gz -R data/test-err-mut-r2.fq.gz -o $tmpdir/test-tmp.sam6 -H -J --rg-id MyTestGroup --rg SM:sample1 --rg TP:1 --rg XX:YY >/dev/null 2>&1 diff --git a/debian/tests/subread-tests b/debian/tests/subread-tests new file mode 100755 index 0000000..c23fe96 --- /dev/null +++ b/debian/tests/subread-tests @@ -0,0 +1,37 @@ +#!/bin/sh + +set -e +pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'` +tmpdir=$(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 +cd $WORKDIR/exactSNP +exactSNP -g ../chr901.fa -o test-out.VCF -i data/test-in.BAM -b >/dev/null 2>&1 + +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 + +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 + +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 -- 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
