Skip to content
Commits on Source (3)
Notes on how this package can be tested.
_______________________________________
This package can be tested by execution
sh run-unit-test
in order to confirm its integrity.
soapdenovo (1.05-5) UNRELEASED; urgency=medium
[ Steffen Moeller ]
* debian/upstream/metadata:
- Added references to registries.
- yamllint clean
[ Liubov Chuprikova ]
* Add autopkgtest
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
-- Steffen Moeller <moeller@debian.org> Wed, 06 Sep 2017 23:50:52 +0200
soapdenovo (1.05-4) unstable; urgency=medium
......
......@@ -5,9 +5,9 @@ Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
rename
Standards-Version: 4.1.0
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/soapdenovo.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/soapdenovo.git
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/soapdenovo
Vcs-Git: https://salsa.debian.org/med-team/soapdenovo.git
Homepage: http://soap.genomics.org.cn/soapdenovo.html
Package: soapdenovo
......
......@@ -39,3 +39,21 @@ License: GPL-2+
.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
Files: debian/tests/test-data/SRR7262809.fastq.tar.gz
Copyright: 1996-2018 NCBI
License: unrestricted
Databases of molecular data on the NCBI Web site include such examples as
nucleotide sequences (GenBank), protein sequences, macromolecular
structures, molecular variation, gene expression, and mapping data. They
are designed to provide and encourage access within the scientific
community to sources of current and comprehensive information. Therefore,
NCBI itself places no restrictions on the use or distribution of the data
contained therein. Nor do we accept data when the submitter has requested
restrictions on reuse or redistribution.
Comment:
The test data files contained in the archive are a small data set prepared
from the original SRA with accession number SRR7262809.
.
To download the original file you can use fastq-dump tool from SRA Toolkit:
fastq-dump --split-3 SRR7262809
MANUAL
debian/tests/test-data
debian/tests/run-unit-test
debian/README.test
debian/tests/test-data/SRR7262809.fastq.tar.gz
Tests: run-unit-test
Depends: @
#!/bin/sh -e
pkg="soapdenovo"
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/test-data/* .
tar -xzvf *.tar.gz; rm *.tar.gz
echo ">>>>>Starting soapdenovo test..."
echo ">>>>>Step 1: pregraph"
soapdenovo-31mer pregraph -s example.config -o graph
[ -s graph.kmerFreq ]
[ -s graph.edge ]
[ -s graph.preArc ]
[ -s graph.vertex ]
[ -s graph.preGraphBasic ]
echo ">>>>>Step 2: contig"
soapdenovo-31mer contig -g graph
[ -s graph.contig ]
[ -s graph.Arc ]
[ -s graph.updated.edge ]
[ -s graph.ContigIndex ]
echo ">>>>>Step 3: map"
soapdenovo-31mer map -s example.config -g graph
[ -s graph.peGrads ]
[ -s graph.readOnContig ]
[ -s graph.readInGap ]
echo ">>>>>Step 4: scaff"
soapdenovo-31mer scaff -g graph
[ -s graph.newContigIndex ]
[ -s graph.links ]
[ -s graph.scaf_gap ]
[ -s graph.scaf ]
[ -e graph.gapSeq ]
[ -s graph.scafSeq ]
echo ""; echo "PASS"; echo ""