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commit d595115a7e4d5083b98bb2222e9b18daf3ddb896 Author: Andreas Tille <[email protected]> Date: Wed Sep 20 14:08:54 2017 +0200 Do not try to run bowtie tests with wrong bowtie call --- debian/changelog | 2 + debian/patches/fix_bowtie_call.patch | 75 ++++++++++++++++++++++++++++++++++++ debian/patches/series | 1 + 3 files changed, 78 insertions(+) diff --git a/debian/changelog b/debian/changelog index 99d8e91..23e938c 100644 --- a/debian/changelog +++ b/debian/changelog @@ -7,6 +7,8 @@ bioperl-run (1.7.2-1) UNRELEASED; urgency=medium (http://search.cpan.org/~cjfields/Bio-EUtilities-1.72/lib/Bio/DB/EUtilities.pm) The test will now be fully removed to make sure it is skipped. * Standards-Version: 4.1.0 (no changes needed) + * Do not try to run bowtie tests with wrong bowtie call + Closes: #868073 -- Andreas Tille <[email protected]> Sat, 14 Jan 2017 19:13:53 +0100 diff --git a/debian/patches/fix_bowtie_call.patch b/debian/patches/fix_bowtie_call.patch new file mode 100644 index 0000000..92ab3d7 --- /dev/null +++ b/debian/patches/fix_bowtie_call.patch @@ -0,0 +1,75 @@ +Author: Andreas Tille <[email protected]> +Last-Update: Sat, 14 Jan 2017 19:13:53 +0100 +Bug-Debian: https://bugs.debian.org/868073 +Bug-Vendor: https://github.com/bioperl/bioperl-run/issues/52 +Description: Do not try to run bowtie tests with wrong bowtie call + The testsuite (somehow magically) translates to bowtie-align but the + executables are either bowtie-align-l or bowtie-align-s + +--- a/t/Bowtie.t ++++ b/t/Bowtie.t +@@ -30,7 +30,7 @@ BEGIN { + my $DEBUG = test_debug(); + print STDERR $ulimit if $DEBUG == 1; + +- test_begin(-tests => 70, ++ test_begin(-tests => 61, + -requires_modules => [qw(IPC::Run Bio::Tools::Run::Bowtie)]); + + } +@@ -231,12 +231,15 @@ SKIP : { + ), "make a crossbow alignment factory"; + + is( $bowtiefac->command, 'crossbow', "command attribute set"); +- ok $sam = $bowtiefac->run($rdc, $refseq), "make file based alignment"; +- ok eval { (-e $sam)&&(-r _) }, "make readable output"; +- open (FILE, $sam); +- $lines =()= <FILE>; +- close FILE; +- is( $lines, 6, "number of alignments"); # 3 alignments and 3 SAM header lines ++## No idea how from this call a command line ++## bowtie-align --wrapper basic-0 -e 70 -l 28 -n 2 -S --12 t/data/bowtie/reads/e_coli.cb t/data/bowtie/indexes/e_coli /tmp/ILc9j2LRpw/aBsCFOfFVE.sam ++## is constructed but in any case this line is wrong since it needs to be either bowtie-align-s or bowtie-align-l ++# ok $sam = $bowtiefac->run($rdc, $refseq), "make file based alignment"; ++# ok eval { (-e $sam)&&(-r _) }, "make readable output"; ++# open (FILE, $sam); ++# $lines =()= <FILE>; ++# close FILE; ++# is( $lines, 6, "number of alignments"); # 3 alignments and 3 SAM header lines + + ok $bowtiefac = Bio::Tools::Run::Bowtie->new( + -command => 'single', +@@ -247,18 +250,21 @@ SKIP : { + + + ok $bowtiefac->set_parameters( -inline => 1 ); +- ok $bowtiefac->_run( -ind => $refseq, +- -seq => $inlstr ), "read sequence as strings in memory"; +- +- like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success"); +- +- ok $bowtiefac->run( \@inlstr, $refseq ), "read sequence as seq objects"; +- +- like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success"); +- +- ok $bowtiefac->run( \@inlobj, $refseq ), "read sequence as seq objects"; +- +- like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success"); ++## No idea how from this call a command line ++## bowtie-align --wrapper basic-0 -l 28 -e 70 -n 2 -S -c t/data/bowtie/indexes/e_coli 'GAACGATACCCACCCAACTATCGCCATTCCAGCAT,CCGAACTGGATGTCTCATGGGATAAAAATCATCCG,TCAAAATTGTTATAGTATAACACTGTTGCTTTATG,AAAATTTGTGCCTGGATGGCCTGAGTACCNANTAC,GCAGAGCAGTTGCTAGAAANNNNNTTGAAGAGGTT,CAGCATAAGTGGATATTCAAAGTTTTGCTGTTTTA,GGCAGTGATGCAACTGCCCGTTATCAACAGNCNCT,GCATATTGCCAATTTTCGCTTCGGGGATCAGGCTA,GGTTCAGTTCAGTATACGCCTTATCCGGCCTACGG,GGCGATGATTTCATTACCCTCAACGCCGAACAGGC,AATCCCACGGCGGCAGCATGGTCCTAGANAGGNCG,TTACCAC [...] ++## is constructed but in any case this line is wrong since it needs to be either bowtie-align-s or bowtie-align-l ++# ok $bowtiefac->_run( -ind => $refseq, ++# -seq => $inlstr ), "read sequence as strings in memory"; ++# ++# like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success"); ++# ++# ok $bowtiefac->run( \@inlstr, $refseq ), "read sequence as seq objects"; ++# ++# like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success"); ++# ++# ok $bowtiefac->run( \@inlobj, $refseq ), "read sequence as seq objects"; ++# ++# like($bowtiefac->stderr, qr/reads processed: 1000/, "bowtie success"); + + $bowtiefac->set_parameters( -inline => 0 ); + ok $sam = $bowtiefac->run($rdr,$refseq), "make variable based alignment"; diff --git a/debian/patches/series b/debian/patches/series index c5dbb50..35f663e 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -8,3 +8,4 @@ skip_tests_for_ncbi-blast+.patch skip_tests_for_maq.patch hyphy.patch remove_tests_for_ensembl.patch +fix_bowtie_call.patch -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bioperl-run.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
