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commit 985aacc4d300c689b223e9b2cc40c8348e2e50e0 Author: Alexandre Mestiashvili <[email protected]> Date: Wed Mar 11 12:26:26 2015 +0100 d/tests/control: add more tests d/tests/exactSNP: use data from source package d/tests/fc-minimal: test_minimal_example.sh d/tests/subjunc: subjunc test --- debian/tests/control | 5 ++++- debian/tests/exactSNP | 19 ++----------------- debian/tests/fc-minimal | 7 +++++++ debian/tests/subjunc | 9 +++++++++ 4 files changed, 22 insertions(+), 18 deletions(-) diff --git a/debian/tests/control b/debian/tests/control index 4b83b61..8d2fc14 100644 --- a/debian/tests/control +++ b/debian/tests/control @@ -1,2 +1,5 @@ Tests: exactSNP -Depends: subread-data + +Tests: fc-minimal + +Tests: subjunc diff --git a/debian/tests/exactSNP b/debian/tests/exactSNP index 4f39039..532b0da 100755 --- a/debian/tests/exactSNP +++ b/debian/tests/exactSNP @@ -1,20 +1,5 @@ #!/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 $testdir/test-in.BAM -b >/dev/null 2>&1 +tmpdir=$(mktemp -d) +exactSNP -g test/chr901.fa -o $tmpdir/test-out.VCF -i test/exactSNP/data/test-in.BAM -b >/dev/null 2>&1 diff --git a/debian/tests/fc-minimal b/debian/tests/fc-minimal new file mode 100755 index 0000000..f57006c --- /dev/null +++ b/debian/tests/fc-minimal @@ -0,0 +1,7 @@ +#!/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 new file mode 100755 index 0000000..9bdf7cf --- /dev/null +++ b/debian/tests/subjunc @@ -0,0 +1,9 @@ +#!/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 -- 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
