Liubov Chuprikova pushed to branch master at Debian Med / soapdenovo
Commits: 2c384317 by Liubov Chuprikova at 2018-06-08T16:09:28+02:00 Add autopkgtest - - - - - 68f684a8 by Liubov Chuprikova at 2018-06-08T16:17:42+02:00 Point Vcs fields to salsa.debian.org - - - - - b96b723e by Liubov Chuprikova at 2018-06-08T16:20:16+02:00 Standards-Version: 4.1.4 - - - - - 9 changed files: - + debian/README.test - debian/changelog - debian/control - debian/copyright - debian/docs - + debian/source/include-binaries - + debian/tests/control - + debian/tests/run-unit-test - + debian/tests/test-data/SRR7262809.fastq.tar.gz Changes: ===================================== debian/README.test ===================================== --- /dev/null +++ b/debian/README.test @@ -0,0 +1,8 @@ +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. ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,9 +1,15 @@ 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 <moel...@debian.org> Wed, 06 Sep 2017 23:50:52 +0200 soapdenovo (1.05-4) unstable; urgency=medium ===================================== debian/control ===================================== --- a/debian/control +++ b/debian/control @@ -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 ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -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 ===================================== debian/docs ===================================== --- a/debian/docs +++ b/debian/docs @@ -1 +1,4 @@ MANUAL +debian/tests/test-data +debian/tests/run-unit-test +debian/README.test ===================================== debian/source/include-binaries ===================================== --- /dev/null +++ b/debian/source/include-binaries @@ -0,0 +1 @@ +debian/tests/test-data/SRR7262809.fastq.tar.gz ===================================== debian/tests/control ===================================== --- /dev/null +++ b/debian/tests/control @@ -0,0 +1,2 @@ +Tests: run-unit-test +Depends: @ ===================================== debian/tests/run-unit-test ===================================== --- /dev/null +++ b/debian/tests/run-unit-test @@ -0,0 +1,44 @@ +#!/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 "" ===================================== debian/tests/test-data/SRR7262809.fastq.tar.gz ===================================== Binary files /dev/null and b/debian/tests/test-data/SRR7262809.fastq.tar.gz differ View it on GitLab: https://salsa.debian.org/med-team/soapdenovo/compare/6ac0f19ef174d5d21400c9cb6ac06d726b055238...b96b723ea0dce1db1cbcf05f2eddebe96ff279ae -- View it on GitLab: https://salsa.debian.org/med-team/soapdenovo/compare/6ac0f19ef174d5d21400c9cb6ac06d726b055238...b96b723ea0dce1db1cbcf05f2eddebe96ff279ae You're receiving this email because of your account on salsa.debian.org.
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