Liubov Chuprikova pushed to branch master at Debian Med / kmer
Commits: e910a4d3 by Liubov Chuprikova at 2018-08-20T08:09:09Z Add autopkgtest - - - - - 9 changed files: - + debian/README.test - debian/atac.docs - debian/changelog - debian/copyright - debian/sim4db.docs - debian/tests/atac-unit-test - debian/tests/control - + debian/tests/sim4db-unit-test - debian/tests/test-data/test_data.tar.gz Changes: ===================================== debian/README.test ===================================== --- /dev/null +++ b/debian/README.test @@ -0,0 +1,14 @@ +Notes on how the packages can be tested in order to confirm their integrity. +____________________________________________________________________________ + +To test atac run: + + sh atac-unit-test + +NOTE: Atac test fails with a segmentation fault. Feel free to use `reportbug +atac` if you have some idea how to fix the test. + +To test sim4db run: + + sh sim4db-unit-test + ===================================== debian/atac.docs ===================================== --- a/debian/atac.docs +++ b/debian/atac.docs @@ -1,3 +1,4 @@ README.atac debian/tests/atac-unit-test debian/tests/test-data/test_data.tar.gz +debian/README.test ===================================== debian/changelog ===================================== --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +kmer (0~20150903+r2013-5) UNRELEASED; urgency=medium + + * Team upload. + * Add autopkgtest. + + -- Liubov Chuprikova <[email protected]> Mon, 20 Aug 2018 09:46:55 +0200 + kmer (0~20150903+r2013-4) unstable; urgency=medium * Team upload. ===================================== debian/copyright ===================================== --- a/debian/copyright +++ b/debian/copyright @@ -36,6 +36,24 @@ Copyright: 2015-2016 Afif Elghraoui <[email protected]> License: GPL-2+ +Files: debian/tests/test-data/test_data.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 were downloaded from NCBI RefSeq + and EST databases using wget and idfetch (from ncbi-tools-bin package): + wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_tuberculosis/latest_assembly_versions/GCF_000195955.2_ASM19595v2/GCF_000195955.2_ASM19595v2_genomic.fna.gz + wget ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/Mycobacterium_leprae/latest_assembly_versions/GCF_000195855.1_ASM19585v1/GCF_000195855.1_ASM19585v1_genomic.fna.gz + idfetch -G EST_GIs.txt -t 5 -o ESTs.fasta + License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by ===================================== debian/sim4db.docs ===================================== --- a/debian/sim4db.docs +++ b/debian/sim4db.docs @@ -1 +1,4 @@ README.sim4db +debian/tests/sim4db-unit-test +debian/tests/test-data/test_data.tar.gz +debian/README.test ===================================== debian/tests/atac-unit-test ===================================== --- a/debian/tests/atac-unit-test +++ b/debian/tests/atac-unit-test @@ -7,9 +7,15 @@ if [ "$AUTOPKGTEST_TMP" = "" ]; then trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM fi cd $AUTOPKGTEST_TMP -cp -a /usr/share/doc/${pkg}/test_data.tar.gz . +cp /usr/share/doc/${pkg}/test_data.tar.gz . tar -xzvf *.tar.gz; rm *.tar.gz # Run atac: -atac -meryldir meryldir -dir results -id1 Ecoli -seq1 GCF_000195995.1_ASM19599v1_genomic.fna \ - -id2 Sent -seq2 GCF_000005845.2_ASM584v2_genomic.fna +atac -meryldir meryldir -dir results -id1 Lepr -seq1 GCF_000195855.1_ASM19585v1_genomic.fna \ + -id2 Tuber -seq2 GCF_000195955.2_ASM19595v2_genomic.fna + +# FIXME! This test fails with the following error message: +# > Segmentation fault +# > Failed to ganerate statistics. + +echo "RESULTS: OK\n" ===================================== debian/tests/control ===================================== --- a/debian/tests/control +++ b/debian/tests/control @@ -1,3 +1,6 @@ +Tests: sim4db-unit-test +Depends: @ + Tests: atac-unit-test Depends: @ Restrictions: allow-stderr ===================================== debian/tests/sim4db-unit-test ===================================== --- /dev/null +++ b/debian/tests/sim4db-unit-test @@ -0,0 +1,23 @@ +#!/bin/sh -e + +pkg="sim4db" + +if [ "$AUTOPKGTEST_TMP" = "" ]; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM +fi +cd $AUTOPKGTEST_TMP +cp /usr/share/doc/${pkg}/test_data.tar.gz . +tar -xzvf *.tar.gz; rm *.tar.gz + +# Run sim4db +echo "Testing sim4 for intra-species alignment...\n" +sim4db -genomic GCF_000195955.2_ASM19595v2_genomic.fna -cdna ESTs.fasta \ + -output results.sim4db +[ -s results.sim4db ] +echo "Testing sim4cc for inter-species alignment...\n" +sim4db -genomic GCF_000195855.1_ASM19585v1_genomic.fna -cdna ESTs.fasta \ + -interspecies -gff3 -output results.gff3 +[ -s results.gff3 ] + +echo "RESULTS: OK\n" ===================================== debian/tests/test-data/test_data.tar.gz ===================================== Binary files a/debian/tests/test-data/test_data.tar.gz and b/debian/tests/test-data/test_data.tar.gz differ View it on GitLab: https://salsa.debian.org/med-team/kmer/commit/e910a4d38d52f5256e55c10dfbbc9fc10dc45250 -- View it on GitLab: https://salsa.debian.org/med-team/kmer/commit/e910a4d38d52f5256e55c10dfbbc9fc10dc45250 You're receiving this email because of your account on salsa.debian.org.
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