Liubov Chuprikova pushed to branch master at Debian Med / genometester
Commits: a304a40c by Liubov Chuprikova at 2018-06-05T23:29:30+02:00 Add autopkgtest. Move manpages to d/man/ - - - - - 15 changed files: - + debian/README.test - debian/changelog - debian/copyright - debian/docs - debian/glistcompare.1 → debian/man/glistcompare.1 - debian/glistmaker.1 → debian/man/glistmaker.1 - debian/glistquery.1 → debian/man/glistquery.1 - debian/gmer_caller.1 → debian/man/gmer_caller.1 - debian/gmer_counter.1 → debian/man/gmer_counter.1 - debian/manpages - + debian/source/include-binaries - + debian/tests/control - + debian/tests/run-unit-test - + debian/tests/test-data/Ccr.fa.gz - + debian/tests/test-data/Mg.fa.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 @@ -1,5 +1,7 @@ genometester (4.0-1) UNRELEASED; urgency=medium * Initial release (Closes: #900752) + * Add manpages + * Add autopkgtest -- Liubov Chuprikova <[email protected]> Mon, 04 Jun 2018 16:33:48 +0200 ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -11,6 +11,20 @@ Files: debian/* Copyright: 2018 Andreas Tille <[email protected]> License: GPL-3+ +Files: debian/tests/test-data/* +Copyright: 2018 EMBL-EBI +License: unrestricted + EMBL-EBI itself places no additional restrictions on the use or redistribution + of the data available via its online services other than those provided by the + original data owners. +Comment: Ensembl Bacteria release 39 + See http://bacteria.ensembl.org/Candidatus_carsonella_ruddii_dc/Info/Index + http://bacteria.ensembl.org/Mycoplasma_genitalium_g37/Info/Index + . + To download the files use: + wget ftp://ftp.ensemblgenomes.org/pub/bacteria/release-39/fasta/bacteria_40_collection/candidatus_carsonella_ruddii_dc/dna/Candidatus_carsonella_ruddii_dc.ASM44157v1.dna.chromosome.Chromosome.fa.gz + wget ftp://ftp.ensemblgenomes.org/pub/bacteria/release-39/fasta/bacteria_13_collection/mycoplasma_genitalium_g37/dna/Mycoplasma_genitalium_g37.ASM2732v1.dna.chromosome.Chromosome.fa.gz + License: GPL-3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by ===================================== debian/docs ===================================== --- a/debian/docs +++ b/debian/docs @@ -1,3 +1,6 @@ README.md README.GenomeTester4.md README.FastGT.md +debian/tests/test-data +debian/tests/run-unit-test +debian/README.test ===================================== debian/glistcompare.1 → debian/man/glistcompare.1 ===================================== ===================================== debian/glistmaker.1 → debian/man/glistmaker.1 ===================================== ===================================== debian/glistquery.1 → debian/man/glistquery.1 ===================================== ===================================== debian/gmer_caller.1 → debian/man/gmer_caller.1 ===================================== ===================================== debian/gmer_counter.1 → debian/man/gmer_counter.1 ===================================== ===================================== debian/manpages ===================================== --- a/debian/manpages +++ b/debian/manpages @@ -1 +1 @@ -debian/*.1 +debian/man/* ===================================== debian/source/include-binaries ===================================== --- /dev/null +++ b/debian/source/include-binaries @@ -0,0 +1,2 @@ +debian/tests/test-data/Ccr.fa.gz +debian/tests/test-data/Mg.fa.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 +1,29 @@ +#!/bin/sh -e + +pkg="genometester" + +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/* . +gunzip *.gz + +echo '---glistmaker test---' +/usr/bin/glistmaker Ccr.fa -o Ccr +/usr/bin/glistmaker Mg.fa -o Mg + +echo '---glistquery test---' +/usr/bin/glistquery Ccr_16.list > Ccr_16.query +/usr/bin/glistquery Mg_16.list > Mg_16.query +[ -s Ccr_16.query ] +[ -s Mg_16.query ] + +echo '---glistcompare test---' +/usr/bin/glistcompare Ccr_16.list Mg_16.list --union -o Ccr_Mg +/usr/bin/glistcompare Ccr_16.list Mg_16.list --intersection -o Ccr_Mg +/usr/bin/glistcompare Ccr_16.list Mg_16.list --difference -o Ccr_Mg +[ -s Ccr_Mg_16_0_diff1.list ] +[ -s Ccr_Mg_16_intrsec.list ] +[ -s Ccr_Mg_16_union.list ] ===================================== debian/tests/test-data/Ccr.fa.gz ===================================== Binary files /dev/null and b/debian/tests/test-data/Ccr.fa.gz differ ===================================== debian/tests/test-data/Mg.fa.gz ===================================== Binary files /dev/null and b/debian/tests/test-data/Mg.fa.gz differ View it on GitLab: https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e -- View it on GitLab: https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e You're receiving this email because of your account on salsa.debian.org.
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