This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic.
commit f22f4d4f71a21c76e36b638d0290dee327ae6026 Author: Sascha Steinbiss <[email protected]> Date: Mon Mar 7 19:41:23 2016 +0000 add autopkgtest --- debian/changelog | 1 + debian/control | 1 + debian/tests/control | 3 + debian/tests/ref.fasta | 200 ++++++++++++++++++++++++++++++++++++++++++++++ debian/tests/test-example | 23 ++++++ 5 files changed, 228 insertions(+) diff --git a/debian/changelog b/debian/changelog index 7a11c9a..60c8cc6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,6 +1,7 @@ snpomatic (1.0-1) unstable; urgency=medium * Use upstream versioning scheme. + * Add autopkgtest. -- Sascha Steinbiss <[email protected]> Mon, 07 Mar 2016 19:21:24 +0000 diff --git a/debian/control b/debian/control index 8c670ac..55a13c4 100644 --- a/debian/control +++ b/debian/control @@ -7,6 +7,7 @@ Build-Depends: debhelper (>= 9), ruby-ronn, antiword Standards-Version: 3.9.6 +Testsuite: autopkgtest Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/snpomatic.git Vcs-Git: git://anonscm.debian.org/debian-med/snpomatic.git Homepage: https://github.com/magnusmanske/snpomatic diff --git a/debian/tests/control b/debian/tests/control new file mode 100644 index 0000000..802ef66 --- /dev/null +++ b/debian/tests/control @@ -0,0 +1,3 @@ +Tests: test-example +Depends: @, samtools +Restrictions: allow-stderr diff --git a/debian/tests/ref.fasta b/debian/tests/ref.fasta new file mode 100644 index 0000000..e4d5a86 --- /dev/null +++ b/debian/tests/ref.fasta @@ -0,0 +1,200 @@ +>ref +taaccctaaccctaaccctgaccctaaccctaaccctaaccctaaccctaaccagtacac +gcgtacacgtacaagcacccgtacccccagtatacctggacacccgtactcagttatcct +ttttattagtgtacccgcctcttgcacgcatgccacagttcttcagcagaagaacacgca +caatgctctttgataaacgtgcggacatgaaaaaaagggaaaaacgcagctacgtgtgct +gtcgttggtttcacagcgtcaagccgcgtcggtgtaccaaagaggaggtgacccatcgag +tactcgcaccctctagctctccttttctgcctcgtattatacacgttgatcggaaaacag +ggtaggcactagccaccgataatcttcaatcgtacatctgtctgcgtaagcgcgtgcccc +ggatggagggcatggaactgcatcgaccgcccacggcgatcgccgatcagccagcgatgt +gactgcaacgctgtttgtttccacaacgagggctgaaggctttctgatagattgtgcgct +atagaacaaggagggagagcccacccctttttatgcgaaaactcctcacccaaagcaagg +agggcggcgggtgggaagcggaaagccaacgcccacgcggacgcaattagcaccgaccga +aaacgagcagtgagaaaaagggaagtctctcagactgggaagagatgagccgaggagata +aatgcaccagatccgaggtaccgcggcacaagaggagccgggtgatattttttgttgttt +tcagtgtttcctcgtgagacggcaaaacacgaggcagaaaaggtgcaagagatccaggtg +gctggcgaagaggaggaacatgagaagagagacagtcaacattggcggggagtcgaactt +tgtgcagctcatgtgtgcaggtgcaggtcgatggatagaaggctaagaggcgataggaca +gggtcccttcacaccacaagcgtgagtgatggagttatatgcgcatggtcgaataggtat +gcacatgtacggcagacaggaaagtagaagagaggaattcggagttgtggagaacgggaa +gtcgatggggcagcagcagcagtcagagcagcagacgaaatgctacacggaacggcttca +cggagagagcatatcagagaagcaggggagctgagaagtgcagtcgatgtgtcacgcttt +gaagtgtgtgacatcaccgaaccgctaccgtgagcaccagaagctcgtctgtgacgaagg +ctccaaagcagatggagaaggaagcaagaccagatggcatgaatcgctcgctttacttta +ccttcgatacgcttactcagtctgttttccggcatcggctcaacaccgccacttgggcaa +ctctctgcgacggcacctacgcgagaccatggcggggtattgttgctttgtttcggagat +ctgcggtatgggtgctgatcatttcaaaacactccagcaatcaagacgaaggaaacacag +accaaagagaagagagacgaagcacggtgagccacgctagccattcatcaacacacccac +acggcaatcacgaaaggcgcaccgcgagagagagagagagagagaacaacggagcctatg +ttgtgagcaaaacaaagtttctcctgatgcataaaacagcaagaaaaagaagagatagct +aaaggacttcgaaagtggaacatcacaccgacgacacggtgtcaaggagaacgagacgga +caaggacgacagaccacatgggagcacaagcgaaactatgacaggtgtgagcaagggcga +atttcctgctgccttgcgactgctggctgatgagcgagtcttctttctttttctccagtt +gtaactgcagcggttgcacgcacgcaagcatgtgaccaccctctcacggttgtcctccat +tgttcgctttctattttttttgtttctcggctcttttagtttcgtcgtgtatctttgcca +accgccgtcatgggttgttgtcttctgccggtatgcctatcgagcgtttttgttttcgtg +cgtgcgtgtgtgtgctcggtgttgtcgttgctcacaaaaagttccccgcggtactgctga +gctgttcacataatgcgcatgtgtctattctgttgctttggtgctcgtggcaccttccga +ggccgccggcgctcacctcctccatgtgcagcggaggcacgcccacggtgggagggaagg +cagcagtggaggctcgtgaggcgacgccgattctgcggtgacattcgcggcgacatcgac +acgttcaatgaagcagttcgacaggacaaggaggccagtaaaaataaaaaatgaaaagaa +gcgtacatgtgacggcagacacatacgccaagagagagagagagagagagcatcgggaag +acggagtcacgcgaaagagaagagcaaaacaaagtagagcacgtggctgtccgttgaata +cgaaggtctccgtgctcgcgactgcatcaccagtagcagcctcatcgttggtcaacgaag +gggaaacaaacaaaaaaaaaaacggaagtgcagagtcgccctcgactaaatcgcgcatag +gcatgccattcatcgatggatgcggagaagcgaagtagtgccgccaaaaactcgacgaag +cctgaccgtcggcaagacgtgacgctcaagggggcggcgcgccacgcgatggagacgaca +ctatgaggtagcggaaaggtagggggagagagagacaagagattctcaaacgaaaacaga +cagtacagaatgagatgggcggagacgcacatgggaggaggacaaagagagacggattac +atgaaacagaccacggatgggtgtcgagaaccaaaaatggagcacaacgagagaaagaag +gttacgagagagatcagaggcatgacaagcagcgccgttctgctctccaccgccgtttcc +tctgtctgcctcgctctctgtcaccgtcgtctttcttttccatgcccctttcaccgctgc +ttcgttgtgctgtgtaccccagatccaaagagcgagcgagagagagagagagaaaaagca +gaaagacaggagagataccgacggaaggagagagtgcagaggagaggcgacacacataag +gcagacacaagaacaataggccgaaagatagggaggaggagggaacagctaaaggtcaca +taaaaagagagaagggggaagatggcagtgcatactggaagcatacgcgcgctctcgctc +tctctcgcgcaaagacacacacacacacacatacacacgcatacatacatacacatatag +atgcccggagagggggaaagcaagggaagcgaaaggagagagctgaaacgtgaaaacgcc +ggaacacggtgtgaagcggagaaggaataggagccaaacagaagaagctatgcagcccaa +caacacgagaaaatgtgtgtgtgtgtgtgtgttcagcgtgtgcgctctactgagagaagg +gcagcccacagacgcccgcacaggcacatagtcgggcgcaaagtggcgattcagtttgcg +cagagagaaaatggggcgatgtggtcgacgtgagcgcacgtcagcagtagcgggccagcg +ggagagaggtgagaagggcaagggaagcaaggcagcagaggcgatgtttctgcagagtcg +cttggtcactgatgcgctgttcttctcttgttcgccctcctgtctactcgcgcgaagagt +acgcatctgcatcggagtcggtgtcgtcggagttgtacatgctggtgcctcggaaagagt +tgtgacggctcagcccgagctccgactgcgtgggaatagcgccctgattatcatactgcg +atccgatgatattacggcggcgcttctcctctttgttgcggcggcggatgcagcagcagc +accagatgctaatgatgagagcaatcaggatgatatagagcacgacggcaatgaggaggc +cgccccaccatgggaacgtttcgttgcacttcgggaggatccagcggctctgcgagtcta +cctcaacctttttgccgcagtacttgtacgtgtggccggagctgctaacgaagggaatgg +cgctgccgcccgggaaggtgggcacaagccgattcacgccatcggagtcggcgtagacgt +agtactcgcagaggaaattcgtaaacgatgtggacacctccgtgttcacccacttcccgg +acggctgcatcacaaccaggcgcttgccccagtagctcaggtttccccaggaacgcgggt +agttggtctcgaaattggtgtaggagcccgacacagcagtagttctgtccactggagtcg +cgtcatcgtttactccccagtagttgacaccgcgcaggaacagcgggcgggtggtgcgga +agagcccgcgataccaccgccactcgcattgggttcccgcgcacaccgcctgctccgtca +tgccgccaagggggatattgccgcgaatgccctcgcgttgataggcactctcgagagcct +cttgaatagaggcggaggtcgacatggccgtgtgcgaccccgcgtcctgcaacttgcaga +aatcgatttctaggggatcgaaggcaaaggccccactgccggcgctgcgcgcggtatacg +ttgtcgagtaggcgtgcgtcattgccggtgcaaaacacgcgagcaccgccacgaccagca +cgaagacgagagcgcagcgcatcttgtcagcagcgggagagaaagacaagcggagaaaac +gaggagagaaagagtgtacgaaatggacgggaacacagacggtggacgagcgagtggtga +tgcgtgagccggcggtgaatgtcgggcgtgagggccgaggggggagaagggaaaaagaca +gtgagccaagaagccgaaaacgaatacgagaggaacgctgaagatcaagcacagtccacc +cccccccctccgcgccggtggtggaaacgctggtgcgtgccggagaagaaccaacaaaaa +caagaaaagcaaggaagcgagagaacggagaaggagaaaggcggggcagtggttgcgcca +agggtccgctaggacttcacggagtacgcacaggtgcagcgggcaagtgcggagacgatg +gggctcatgtgtggcaggggaagatgggaagaacgaaaagggaggaggtgtggaagaggg +tagaagtgttctctgtgagtaatagcacaggcaatccatctcacgggagagatgagggag +gatgcaaagtcgcggccgcgtggcgagtatgcggggcgtggttcacgctcctcacatgtc +ggtgcctgggctgtctttcccagtgttgtaggtgatgcctgagcaaggagcagcatcctg +agggctcataaggagaggaggagcacaaccgtaggggtagtcgcacgccttcatgcgctg +ttggcggggctgtgcaaagtgaaccacactaggcgagtggcagacgccagcgaaggccat +ggtggctaggggtacgaggcgagttaacggtcgccctgttgtgttctcccgttgccgcag +cagccactcctccctcgtcgcccatttgatgctctcgaatcgtctatgggtgagggttct +cgtctgcacgaccaggcgcgggcagtgatgatgtcccgcgtgtcagtgagggcgcatgcg +tgcggtgcggcacaatgggcttgtcggtatcccgtatgtgagcatggaaagacaaaccgc +cagcgacaacaacaactcgaatcagcgaggaagccagtagaggcacacaggcacagacac +acggaacacgcactctcacccctatgcgcctattctttcaacgttcgtgcggcgacatcg +gggaaggagtcgatccaggagatgtcgatgaagagcggaaggtggtgggaaggcagcttg +tggttaggaaagagttgcgcctcgttcacctcctcatcctcaggaacgtccagcacctga +tgcagggcgagcgtgctggggtcgtagaaaatgaagtcctgtgtgttgtacgtgatgcct +ttcgcctttcggctctccttcaagagcgcaagctggtcgaccctgacggcggtgtcagac +ggcgctggtgcggaggctggcgatggcgccggtgcagcagcaacggtgtcagcaggcgga +ggtgtcgccacctctggcgcagtctttggcgtcgtcagctgctgttgttgcttcttgtga +gcccgagccgcgatctcgtcccgcacaagccgcactttggagaagacgccatggtagcca +cccgcgtccttgcgccggaaacggtggatctcctcctcggcctggtaggccttgtcggag +cggtgagcctgctccacgttctttgtgtagtacgtgtcataggcggcggcgcgggcgtcg +tctcggtagtgccacgccgtccagcgcggcccgccaaccaggtcatgcgtggaaaaaaat +ctgtcgcgcaggagctccacgcacggctcatcgtccgcttgattgttcaggtcgccacag +acgatgtgcgactgatgcgagcgatctgcgtcgtttcggccgagggcatcaagtatggtg +agcacctgtcgtgcctcgtgcagccggacgtcggccgcctctgccgtcgcccccgcggtg +agctgcacgcaggcgacgtagagggtcatgtttgtcactttgtcccgcatgccgacgaag +tgcgcaaagtggaagcgctggccgatatcgcggccaggcatcatgagcgggaaaaagcgg +cccttgtgaaacagaagcacgttgccgatgtcctcctcctcggcgatcttgccctggtta +gacggagcggcggcattgtcacccttgcggagtgcccgcacctgggcaccacggctggac +tggtagagcgtgccgtagccgaggaaacgtacatatcgccacaactcggtgttgaaaaag +gtccgcttcacctcgttcaagcaggcgatatcggggtcgtagcaccgaagcagctccacg +aggtgcttgcgacggtgctccggcgtgaggaagggtgggaactccttgtcgatggagggg +tcgtagtcgcagcaggcgttggggtcgtcgcattccgggttgcgggtgaactcgggcacg +cgcacccgcaccgcctctacgggggtggtgtgaccgggcccccaggcgtccgtcatcatg +ttgaagctcatcaggcggaaccaatcacgccgtgagaggctcgtcgacagctgagagacg +ggcgccttcacccacttgcgcttcagcggaggctcgcgctccgcctccatcttctccgct +tgcatctcgcgcgctagcaggctcgacatcttcacctccagcgcgctctgcgcgatctgc +gcgtccatgatggaggggcggatcgttgtgcgcgtgccggtgtcccgcatcagacccacg +accgggccaccgctcaccagtggcggatcattcagtagcactgagcagcgtctcaacatc +tacagaagaggagggcggcgaagggaatcactgcatgaggcatgcgacgctcgaagatgg +cgaaacacggcccgctctgtgcgaccgtgcgtaggtcggtcggtgtgagcgaggtgtttg +caggggggacacttcacagtccggagcagacgaataagcggagggaaggagggagggata +ggaggggggcactgatgcggtggcatacgtagccccgcagaaatacgggagatgacgggg +gagagaggaggagtaggatagacggtcgtgaaggatgagagaaaaagtgcacaagacggc +acgacacgttcgtgtgtggctttcaggggcacacaggaggcatgcgcaaaagcatacgcg +gcacagtcggcaatcaacaacccgcgcgtctctctctctctctctgcagaacattgctac +ccttgcgccatctgttgatgccgttgaggaggcctccagctgctgcacccctggcagccg +caccgacctcacgtgaatacccccgtccacactggcctctacttgtccttctacgcgggg +gacgaggtgactttgtgcgcatgtggcggttgccttctcgcttccccgtcttccgtgtgc +ggaggaggggtcgagggcgcaaagacgtccgaaggagagtagaggagagggcgtagatgg +caagggccttacaacaggcacacagacaaccacagatgcgccgtgttgggggttgagcga +ggcgtgagagagggagcgagaagccgaagagacaagacatgaaaacatcgaaaatggaag +agagctaaaacgcatgccatcacaggcacacgtgcacatacacatggagagagggagaga +caacggcttcttcgcggtcgcctttccacaagcgtattgttgcgggcaacagcagggggg +ttgcttctaggccgctggagctggacgtgcgtcggagagctggaaggcacagaggccagc +ggcattggttttgccagtgctggatgcagacgttgctcaaggatagatgcagagaggtag +agagtgagtggccgcacggggcacgcagaaagaatgtccgcatggaggaagaagcagcgc +ccacacgtccaatgcacaagagcaccgcccgaatcgatgaggccaagaaagaggaggagc +aacggccatcgactgcagctgcgtgaggctgcggctgaggctgtggggggagggagggga +gttgcatctacgtctaacatgataggagagaaaaacgaacaccgaacggtatgccacaca +catacacacacacggacagacaggcagagagcacgagagagcgaaaacggaaagagggga +gcgcaagcgatgaaagagagcgtccgagtctaaaacagcggcgaccgcaaacacgcgagc +ggtcaccacgaacagagagagcccgagcccactaaagctggtaaaggaccggaagcggca +cacagcgcctcgaacgaagcacctgcacggcagcaccggtgctgatggccaaacacacac +gcacgcgcagacacgcatgaataaaaaaaaaatgatagagaagacacatgcgcgaaaggt +gcagcgaacaccgacaacacgaaaaagaaagggcgatacctagaaggacgatgaacacgg +ctacgttggcggcaggtgctgctgaaaggcggtgatgtcggcgacctgctgcgcgatctt +gtcgagctcctccagctgcgttaggaaggactccatcgcgcgccgtttctcgctcaccag +cagacgtgcgcgctccacaaagctgcgcgtgttggcgttcatctgctctgcgtcgtactt +cacctggtactcctccttgatacagttcatgtccgtctcgaggtaggcgttgtattggtc +aatgacgcgactgcgctgggccgcgacaagctcggcgccgctctcgaagcgcttgaagct +tgggcgcccactcggccgcgctaccacttcgtcctcgccgcttctgtctgagtcgcgggg +ccgcttagtgcacaccatgtccggagtccgatcgcgcgacggcggcttcggggtgacgag +agtcgacttggcctgcgacgacggcgagagtgtgttgacggagcggctgctgagtagcgt +gcttctaagtgctggcgcagccgtcgaagagccggagaaaagcggggcggccgtagaaag +gcgagttgtcgtcctccgcgacggtggcctgctctcggtcgtgtcaaagaaggcctcttc +ctggtcgtcgggcatgcacacagtgcgccgctccgtggcgttgcgcttcagctccttgac +acgatcggcgtagcgcagcgtgttcagcgtgtgctcggcattgttgttcgacggagagac +ggcgccgatcatcaccgtgcggcagttgccgataaacgagtcgcggagcacctcagtcag +cttcgagccgcggaacgggacgtgcttcctgttctgatctaaaaaacgaatgcactcctt +cagcgcgagtaggctcttgttgatctccgccccttcgaggcgtgtctgtcgcgcgcagtc +caccgtgtcagcgccgcgctcgcttccagcgaggtcgatgaacgtgaacttgccgctctg +cttcgacgtccgtttcgccttgagcttgatctcgagaatggcgtgggagcgggagcttgt +gtcattggcgccggtggagccgcagctgcgaacaccgctgccctggtcgatgatcgtcat +gaggtcctccacgctggtagagcagtgttcggtgaggccgcggatgttcacccggccctt +gtcgtcctcgagggctcgcaggggtcgccggccgttcagcaagtcaaagagcttcccgct +gtagatctcgtaaaaggaaacgacgatgcgcgtgtcgctcgtgaggcggtcaaacatgtc +tttggcggcgagtgcgtagaggcccggctcggggcccttgcccagcatcgtgtgtgtctt +gccgctccctgtctgtccataggcgaagcatgtcgcgcagccgccgtcgaagacggtgtc +gatcagcgcgcgggcagcgcggttgtacacgtcgacgttgtcgcaggcctcgtcgaaaac +ctcgtcgaagaagaagcggtgcacgtgggtgtacttgcggaggtcgaccttcacctttgg +ctccttcagcacaatctcgccgctgttgtcggcgtccatgatgtccgtgaagccgttcgt +ctgctccccggcgctgagcggacgcttgcgaatggcgacgaggatgcggctcttgcgctt +cacctcctcggcggtgtcggtcgaccggcaaaggactgtggttccgcgtgctgtgtactg +ccgccggcgctccgtcgagcacccctccttcccctccggcgtactgtcgtcgccctcgcc +gtcgccgtcgccgtcgttgtcgagcacgtcactgccagagcgcgaggcggggagcggatt +agccttgatgtactcgatggcgtcacgcagccgcaaaatgtccatcgcctctacgacgcc +gtagcggttgaagtcctctggctgcagggcgaggaggtccttgatggtcatgctcgatgc +aaaggcacactgaaagcgctccagctggtaccgccgcagcacgtcgctgatgtacggctg +cgacgacggcggctcggccgacatcatctgcgacgcactggccgtcacgctcacaaattt +acggacgcttcgcgaggaaaggggaggagagcgtcaacaaagaaagagtctaagatgggg +cagagagagacgcgaggaagcagccgaagcggcctgggtgccgcgggtcctttgccgcca +ccgatgtggagagaagacgagcggggagtcgagcaggcggtgactgacggtcggcgcact +tgcttgcgtcgcgctcaggcagctcgtagaagcggaggaggacacggagaagaaggaaaa +gggacggagacgatgatgcgcgtgcgtgcgcatgaaaaggtgcctcgtggtgcagatgcg +ggatctgcagtaagaagtgcggcggtgcgtcgtgcgaacgtctctgtatgaggatggcag +cgaggagagaacgagagacggacacagacaacggaaggaggacgtgtgcacctgtatgca +tgcatgcatgcgtgtgttttctgtgaatgtgcgtgtgtgtgtgtgtgtgtgtgtgtgtgt +gtgtgtgcgtactcgtactcgccctcactcgcctcgctcgcagatggtacggaggcgaag +gggtgctgtcgaggactagggtgtggtgcgagggcgtcagacggtcccgttgatgggcgg +gtgtgtaacaggcaacagcgagatgggaagcgaatacggagagagcaggaggaggatggg +aatggtgatggtcggcgtcgtcgtcgtcgtcgtggtgccatgggtgaaagcggcagcggt +gccgtatgcgccctccacgcatcgggcagagtgcgatcgcagcagttgactgtcactact +tgcccgcgcctaagaggcctgagaaggagggcaggggtgtgtgaatctcccacagggaca diff --git a/debian/tests/test-example b/debian/tests/test-example new file mode 100755 index 0000000..4f9f8cc --- /dev/null +++ b/debian/tests/test-example @@ -0,0 +1,23 @@ +#!/bin/sh +# autopkgtest check: Run simulated test data through snpomatic +# Author: Sascha Steinbiss <[email protected]> +set -e + +ORIGDIR=$(pwd) +DATADIR=$ORIGDIR/debian/tests/ +WORKDIR=$(mktemp -d) + +trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM +cd $WORKDIR + +cp $DATADIR/ref.fasta . +wgsim -N 10000 -r 0.01 -S 42 \ + ref.fasta \ + reads.1.fq \ + reads.2.fq +findknownsnps --genome=ref.fasta \ + --fastq=reads.1.fq \ + --gffout=out.gff \ + --fastq2=reads.2.fq + +[ -s out.gff ] -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
