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commit 56eb7e4f2b68bda9cc935d0ec22ea11c421f8e82 Author: Alexandre Mestiashvili <[email protected]> Date: Fri Mar 13 14:45:27 2015 +0100 d/control: update Description for subread-data d/subread-data.install: install test directory into examples dir d/tests/exactSNP: modify test to use data from the examples dir --- debian/control | 16 +++++++++------- debian/subread-data.install | 1 + debian/tests/exactSNP | 13 ++++++++++++- 3 files changed, 22 insertions(+), 8 deletions(-) diff --git a/debian/control b/debian/control index 25b7c15..59303b2 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 @@ -23,11 +23,13 @@ Description: tool kit for processing next-gen sequencing data alignments and Subjunc performs global alignments. Package: subread-data -Architecture: all +Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: data files for subread package - This package provides the annotation directory from the original tarball - which includes NCBI RefSeq gene annotations for genomes 'hg19', 'mm10' - and 'mm9'. Each row is an exon. Entrez gene identifiers and chromosomal - coordinates are provided for each exon. + This package provides data files from the original tarball: + - annotation: Directory including NCBI RefSeq gene annotations for + genomes 'hg19', 'mm10' and 'mm9'. Each row is an exon. + Entrez gene identifiers and chromosomal coordinates are provided for + each exon. + - test: Directory including test data and scripts. diff --git a/debian/subread-data.install b/debian/subread-data.install index ae2db19..10b1661 100644 --- a/debian/subread-data.install +++ b/debian/subread-data.install @@ -1 +1,2 @@ annotation usr/share/doc/subread/examples +test usr/share/doc/subread/examples diff --git a/debian/tests/exactSNP b/debian/tests/exactSNP index 532b0da..52f6177 100755 --- a/debian/tests/exactSNP +++ b/debian/tests/exactSNP @@ -1,5 +1,16 @@ #!/bin/sh set -e +pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'` tmpdir=$(mktemp -d) -exactSNP -g test/chr901.fa -o $tmpdir/test-out.VCF -i test/exactSNP/data/test-in.BAM -b >/dev/null 2>&1 +examplesdir=/usr/share/doc/$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 -- 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
