Étienne Mollier pushed to branch master at Debian Med / bioperl-run
Commits: ac21737c by Étienne Mollier at 2020-12-04T23:19:02+01:00 add get-overlap.patch It maps "betools overlap" to "getOverlap". - - - - - 8dc23c6f by Étienne Mollier at 2020-12-04T23:21:23+01:00 build depend on bedtools datasets - - - - - 61b1a5ae by Étienne Mollier at 2020-12-04T23:28:12+01:00 add alternate-data.patch - - - - - 5 changed files: - debian/changelog - debian/control - + debian/patches/alternate-data.patch - + debian/patches/get-overlap.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -16,6 +16,12 @@ bioperl-run (1.7.3-5) UNRELEASED; urgency=medium * debhelper-compat 13 (routine-update) * Remove trailing whitespace in debian/control (routine-update) + [ Étienne Mollier ] + * Add get-overlap.patch to map to the proper "getOverlap" wrapper. + * Add build time test dependencies to get BEDtools test data sets. + * Add alternate-data.patch to use a dataset available in the Debian + archive during build time testings. + -- Andreas Tille <[email protected]> Thu, 03 Dec 2020 21:57:37 +0100 bioperl-run (1.7.3-4) unstable; urgency=medium ===================================== debian/control ===================================== @@ -28,6 +28,7 @@ Build-Depends-Indep: perl, # Needed for the regression tests: all Recommends of bioperl-run except embassy, that needs interactive setup. amap-align, bedtools, + bedtools-test, ncbi-blast+-legacy, clustalw, emboss, @@ -43,6 +44,7 @@ Build-Depends-Indep: perl, phyml, primer3, probcons, + python3-pybedtools, raxml, samtools, sim4, ===================================== debian/patches/alternate-data.patch ===================================== @@ -0,0 +1,32 @@ +Description: use alternate rmsk dataset + This patch solves the following test suite error, occurring even though BED + tools are made available at build time testing: + . + ------------- EXCEPTION: Bio::Root::Exception ------------- + MSG: File '' not BED/GFF/VCF format. + STACK: Error::throw + STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449 + STACK: Bio::Tools::Run::BEDTools::run /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/BEDTools.pm:477 + STACK: t/BEDTools.t:252 + ----------------------------------------------------------- + . + Instead of using the default rmsk.hg18.chr21.bed file which is unavailable in + the archive, let's use rmsk.hg18.chr21.small.bed, provided by the package + python3-pybedtools, which seemingly does the job almost as well apparently. +Author: Étienne Mollier <[email protected]> +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=974168 +Forwarded: no +Last-Update: 2020-12-04 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- bioperl-run.orig/t/BEDTools.t ++++ bioperl-run/t/BEDTools.t +@@ -182,7 +182,7 @@ + chdir $dir; # Go back to $dir; + } + else { +- ($rmsk_bed) = `find /usr -name 'rmsk.hg18.chr21.bed' 2>/dev/null`; ++ ($rmsk_bed) = `find /usr -name 'rmsk.hg18.chr21.small.bed' 2>/dev/null`; + ($gene_bed) = `find /usr -name 'knownGene.hg18.chr21.bed' 2>/dev/null`; + ($mm8_genome) = `find /usr -name 'mouse.mm8.genome' 2>/dev/null`; + ($mm9_genome) = `find /usr -name 'mouse.mm9.genome' 2>/dev/null`; ===================================== debian/patches/get-overlap.patch ===================================== @@ -0,0 +1,33 @@ +Description: change mapping of bedtools subcommand overlap + This patch addresses the following test error: + . + # Failed test 'get version for 'overlap'' + # at t/BEDTools.t line 212. + . + ------------- EXCEPTION: Bio::Root::Exception ------------- + MSG: No executable! + STACK: Error::throw + STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449 + STACK: Bio::Tools::Run::BEDTools::run /<<PKGBUILDDIR>>/blib/lib/Bio/Tools/Run/BEDTools.pm:278 + STACK: t/BEDTools.t:275 + ----------------------------------------------------------- + . + Config.pm assumes the subcommand of bedtools "overlap" is called "overlap", but + it is actually "getOverlap". +Author: Étienne Mollier <[email protected]> +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=974168 +Forwarded: no +Last-Update: 2020-12-04 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- bioperl-run.orig/lib/Bio/Tools/Run/BEDTools/Config.pm ++++ bioperl-run/lib/Bio/Tools/Run/BEDTools/Config.pm +@@ -134,7 +134,7 @@ + 'links' => 'linksBed', + 'pair_to_pair' => 'pairToPair', + 'subtract' => 'subtractBed', +- 'overlap' => 'overlap', ++ 'overlap' => 'getOverlap', + 'group_by' => 'groupBy', + 'graph_union' => 'unionBedGraphs' + ); ===================================== debian/patches/series ===================================== @@ -12,3 +12,5 @@ skip_tests_for_ncbi-blast+.patch hyphy.patch remove_tests_for_ensembl.patch skip_tests_for_soap.patch +get-overlap.patch +alternate-data.patch View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7d8c9a8542ae51ea7e538a327da35a675227b933...61b1a5aed7046d17ede7f01d5f9ffab82b5ad1ea -- View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7d8c9a8542ae51ea7e538a327da35a675227b933...61b1a5aed7046d17ede7f01d5f9ffab82b5ad1ea You're receiving this email because of your account on salsa.debian.org.
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