[med-svn] [Git][med-team/bioperl-run][master] 3 commits: add get-overlap.patch
Étienne Mollier
gitlab at salsa.debian.org
Fri Dec 4 22:28:38 GMT 2020
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 <tille at debian.org> 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 <etienne.mollier at mailoo.org>
+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 <etienne.mollier at mailoo.org>
+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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20201204/c5c2e5d0/attachment-0001.html>
More information about the debian-med-commit
mailing list