[med-svn] [subread] 01/04: 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

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository subread.

commit 56eb7e4f2b68bda9cc935d0ec22ea11c421f8e82
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
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 <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
@@ -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

-- 
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