Liubov Chuprikova pushed to branch master at Debian Med / soapdenovo2
Commits: ad5c6e10 by Liubov Chuprikova at 2018-06-12T18:28:44+02:00 Add autopkgtest - - - - - 8 changed files: - + debian/README.test - debian/changelog - debian/copyright - debian/docs - + debian/source/include-binaries - + debian/tests/control - + debian/tests/run-unit-test - + debian/tests/test-data/SRR2480581.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 @@ -1,3 +1,10 @@ +soapdenovo2 (241+dfsg-3) UNRELEASED; urgency=medium + + * Team upload. + * Add autopkgtest + + -- Liubov Chuprikova <[email protected]> Tue, 12 Jun 2018 17:35:14 +0200 + soapdenovo2 (241+dfsg-2) unstable; urgency=medium * debian/upstream/metadata: ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -79,3 +79,21 @@ 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/SRR2480581.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 SRR2480581. + . + To download the original file you can use fastq-dump tool from SRA Toolkit: + fastq-dump --split-3 SRR2480581 ===================================== debian/docs ===================================== --- a/debian/docs +++ b/debian/docs @@ -1 +1,4 @@ README.md +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/SRR2480581.fastq.tar.gz ===================================== debian/tests/control ===================================== --- /dev/null +++ b/debian/tests/control @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== --- /dev/null +++ b/debian/tests/run-unit-test @@ -0,0 +1,47 @@ +#!/bin/sh -e + +pkg="soapdenovo2" + +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 soapdenovo2-63mer test..." +echo ">>>>>Step 1: pregraph" +soapdenovo2-63mer pregraph -s example.config -o graph +[ -s graph.kmerFreq ] +[ -s graph.edge.gz ] +[ -s graph.preArc ] +[ -s graph.vertex ] +[ -s graph.preGraphBasic ] + +echo ">>>>>Step 2: contig" +soapdenovo2-63mer contig -g graph +[ -s graph.contig ] +[ -s graph.Arc ] +[ -s graph.updated.edge ] +[ -s graph.ContigIndex ] + +echo ">>>>>Step 3: map" +soapdenovo2-63mer map -s example.config -g graph +[ -s graph.peGrads ] +[ -s graph.readOnContig.gz ] +[ -s graph.readInGap.gz ] + +echo ">>>>>Step 4: scaff" +soapdenovo2-63mer scaff -g graph +[ -s graph.newContigIndex ] +[ -s graph.links ] +[ -s graph.scaf_gap ] +[ -s graph.scaf ] +[ -e graph.gapSeq ] +[ -s graph.scafSeq ] + +# soapdenovo2-127mer testing requires lots of memory->Skipped + +echo ""; echo "PASS"; echo "" ===================================== debian/tests/test-data/SRR2480581.fastq.tar.gz ===================================== Binary files /dev/null and b/debian/tests/test-data/SRR2480581.fastq.tar.gz differ View it on GitLab: https://salsa.debian.org/med-team/soapdenovo2/commit/ad5c6e10dd11bfe2cd51514f7c759631f5e6c99c -- View it on GitLab: https://salsa.debian.org/med-team/soapdenovo2/commit/ad5c6e10dd11bfe2cd51514f7c759631f5e6c99c You're receiving this email because of your account on salsa.debian.org.
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