[med-svn] r15203 - in trunk/packages/bioperl-run/trunk/debian: . patches source
Andreas Tille
tille at moszumanska.debian.org
Wed Nov 20 21:58:35 UTC 2013
Author: tille
Date: 2013-11-20 21:58:35 +0000 (Wed, 20 Nov 2013)
New Revision: 15203
Added:
trunk/packages/bioperl-run/trunk/debian/source/
trunk/packages/bioperl-run/trunk/debian/source/format
Removed:
trunk/packages/bioperl-run/trunk/debian/README.source
Modified:
trunk/packages/bioperl-run/trunk/debian/changelog
trunk/packages/bioperl-run/trunk/debian/compat
trunk/packages/bioperl-run/trunk/debian/control
trunk/packages/bioperl-run/trunk/debian/copyright
trunk/packages/bioperl-run/trunk/debian/patches/Some-spellchecking.patch
trunk/packages/bioperl-run/trunk/debian/patches/Use-system-s-Perl.patch
trunk/packages/bioperl-run/trunk/debian/patches/install-scripts.patch
trunk/packages/bioperl-run/trunk/debian/rules
trunk/packages/bioperl-run/trunk/debian/watch
Log:
Mass commit for 1.6.9-2
Deleted: trunk/packages/bioperl-run/trunk/debian/README.source
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/README.source 2013-11-20 21:58:05 UTC (rev 15202)
+++ trunk/packages/bioperl-run/trunk/debian/README.source 2013-11-20 21:58:35 UTC (rev 15203)
@@ -1,8 +0,0 @@
-This package uses quilt to patch the sources. Please refer to
-/usr/share/doc/quilt/README.source for more informations.
-
-This package is maintained by the Debian Med packagign team. Please refer to
-our group policy if you would like to commit to our Subversion repository. All
-Debian developpers have write acces to it.
-
-http://debian-med.alioth.debian.org/docs/policy.html
Modified: trunk/packages/bioperl-run/trunk/debian/changelog
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/changelog 2013-11-20 21:58:05 UTC (rev 15202)
+++ trunk/packages/bioperl-run/trunk/debian/changelog 2013-11-20 21:58:35 UTC (rev 15203)
@@ -1,3 +1,19 @@
+bioperl-run (1.6.9-2) unstable; urgency=low
+
+ * debian/source/format: 3.0 (quilt)
+ * debian/control:
+ - cme fix dpkg-control
+ - canonical Vcs URLs
+ - debhelper 9
+ * debian/README.source: removed because redundant
+ * debian/copyright: DEP5
+ * debian/watch: Point download location to github which provides more
+ reliable version numbering than CPAN which would have needed a more
+ complex version mangling
+ * refreshed quilt patches to get rid of fuzz
+
+ -- Andreas Tille <tille at debian.org> Fri, 15 Nov 2013 10:03:29 +0100
+
bioperl-run (1.6.9-1) unstable; urgency=low
* New upstream release.
Modified: trunk/packages/bioperl-run/trunk/debian/compat
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/compat 2013-11-20 21:58:05 UTC (rev 15202)
+++ trunk/packages/bioperl-run/trunk/debian/compat 2013-11-20 21:58:35 UTC (rev 15203)
@@ -1 +1 @@
-8
+9
Modified: trunk/packages/bioperl-run/trunk/debian/control
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/control 2013-11-20 21:58:05 UTC (rev 15202)
+++ trunk/packages/bioperl-run/trunk/debian/control 2013-11-20 21:58:35 UTC (rev 15203)
@@ -1,59 +1,136 @@
Source: bioperl-run
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 8), quilt, libmodule-build-perl
-Build-Depends-Indep: perl, bioperl (>= 1.6.9),
+Build-Depends: debhelper (>= 9)
+Build-Depends-Indep: perl,
+ bioperl (>= 1.6.9),
# Recommended in Build.PL:
- libalgorithm-diff-perl,
- libipc-run-perl,
- libio-string-perl,
- libxml-twig-perl,
+ libalgorithm-diff-perl,
+ libipc-run-perl,
+ libio-string-perl,
+ libxml-twig-perl,
# Not yet available: libfile-sort-perl
# Needed for the tests, but not documented Upstream
- libarray-compare-perl, libtree-dagnode-perl,
+ libarray-compare-perl,
+ libtree-dagnode-perl,
# Needed for the regression tests: all Recommends of bioperl-run except embassy, that needs interactive setup.
# amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate,
# hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probcons,
# samtools, sim4, t-coffee, tigr-glimmer, wise,
# Needed for the network tests:
- libwww-perl
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>
-Standards-Version: 3.9.2
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bioperl-run/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bioperl-run/trunk/
+ libwww-perl
+Standards-Version: 3.9.4
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/bioperl-run/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/bioperl-run/trunk/
Homepage: http://www.bioperl.org/wiki/Run_package
Package: bioperl-run
Architecture: all
-Depends: ${misc:Depends}, ${perl:Depends}, bioperl (>= 1.6.0), libbio-perl-run-perl (= ${source:Version})
-Recommends: amap-align, bedtools, blast2, bowtie, bwa, clustalw, emboss, exonerate,
- hmmer, infernal, kalign, maq, mafft, muscle, phyml, primer3, probcons,
- samtools, sim4, t-coffee, tigr-glimmer, wise
-Suggests:
+Depends: ${misc:Depends},
+ ${perl:Depends},
+ bioperl,
+ libbio-perl-run-perl (= ${source:Version})
+Recommends: amap-align,
+ bedtools,
+ blast2,
+ bowtie,
+ bwa,
+ clustalw,
+ emboss,
+ exonerate,
+ hmmer,
+ infernal,
+ kalign,
+ maq,
+ mafft,
+ muscle,
+ phyml,
+ primer3,
+ probalign,
+ probcons,
+ samtools,
+ sim4,
+ t-coffee,
+ tigr-glimmer,
+ wise
+Suggests:
# Non-Free.
- gmap, paml, molphy, phylip,
-# Not available.
-# blat, cap3, coils, condense, drawgram, drawtree, eponine, fasta, footprinter, genemark-hmm,
-# genscan, gerp, glimmer2, hyphy, lagan, lvb, match, mcs, mdust, meme, minimo,
-# neighbor, newbler, njtree, pal2nal, phastcons, phrap, primate, prints, probalign, profile,
-# promoterwise, protdist, protpars, pseudowise, quikctree, repeatmasker, sablastplus, seg,
-# semphy, seqboot, signalp, simprot, slr, soapeu, tigr-assembler, tmhmm, tribe, trnascan, vista-align,
-# Available, but needs interactive setup.
- ensembl
+ gmap,
+ paml,
+# Removed from Debian at all molphy,
+# Removed from Debian but might be reintroduced ensembl,
+ phylip
+# The following list of packages is not available in Debian:
+# blat,
+# cap3,
+# coils,
+# condense,
+# drawgram,
+# drawtree,
+# eponine,
+# fasta, # non-free, inofficial package for BioLinux
+# footprinter,
+# genemark-hmm,
+# genscan,
+# gerp,
+# glimmer2,
+# hyphy,
+# lagan, # packaging work in progress
+# lvb,
+# match,
+# mcs,
+# mdust,
+# meme, # non-free, packaging work in progress
+# minimo,
+# neighbor,
+# newbler,
+# njtree,
+# pal2nal,
+# phastcons,
+# phrap,
+# primate,
+# prints,
+# profile,
+# promoterwise,
+# protdist,
+# protpars,
+# pseudowise,
+# quikctree,
+# repeatmasker,
+# sablastplus,
+# seg,
+# semphy,
+# seqboot,
+# signalp,
+# simprot,
+# slr,
+# soapeu,
+# tigr-assembler,
+# tmhmm,
+# tribe,
+# trnascan,
+# vista-align
Description: BioPerl wrappers: scripts
Contains scripts from the BioPerl-Run package. This package will also install
all wrappable applications packaged in Debian. The ones that are not Free are
"Suggested" by this package.
Package: libbio-perl-run-perl
+Architecture: all
Section: perl
-Architecture: all
+Depends: ${misc:Depends},
+ ${perl:Depends},
+ libbio-perl-perl
+Recommends: libalgorithm-diff-perl,
+ libipc-run-perl,
+ libio-string-perl,
+ libxml-twig-perl,
+ libwww-perl
Breaks: bioperl-run (<< 1.6.9)
Replaces: bioperl-run (<< 1.6.9)
-Depends: ${misc:Depends}, ${perl:Depends}, libbio-perl-perl (>= 1.6.0)
-Recommends: libalgorithm-diff-perl, libipc-run-perl, libio-string-perl, libxml-twig-perl, libwww-perl
Description: BioPerl wrappers: modules
Contains modules that provide a Perl interface to various bioinformatics
applications to allow them to be used with common BioPerl objects.
Modified: trunk/packages/bioperl-run/trunk/debian/copyright
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/copyright 2013-11-20 21:58:05 UTC (rev 15202)
+++ trunk/packages/bioperl-run/trunk/debian/copyright 2013-11-20 21:58:35 UTC (rev 15203)
@@ -1,4 +1,4 @@
-Format: http://dep.debian.net/deps/dep5/
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.006900.tar.gz
Files: *
Modified: trunk/packages/bioperl-run/trunk/debian/patches/Some-spellchecking.patch
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/patches/Some-spellchecking.patch 2013-11-20 21:58:05 UTC (rev 15202)
+++ trunk/packages/bioperl-run/trunk/debian/patches/Some-spellchecking.patch 2013-11-20 21:58:35 UTC (rev 15203)
@@ -26,11 +26,9 @@
t/lib/Test/Builder/Tester.pm | 2 +-
19 files changed, 26 insertions(+), 26 deletions(-)
-diff --git a/lib/Bio/Tools/Run/Alignment/Clustalw.pm b/lib/Bio/Tools/Run/Alignment/Clustalw.pm
-index 2295987..e9afe69 100644
--- a/lib/Bio/Tools/Run/Alignment/Clustalw.pm
+++ b/lib/Bio/Tools/Run/Alignment/Clustalw.pm
-@@ -205,7 +205,7 @@ clustalw program have not yet been implemented. If you would like
+@@ -205,7 +205,7 @@ clustalw program have not yet been imple
that a specific clustalw feature be added to this perl contact
bioperl-l at bioperl.org.
@@ -39,8 +37,6 @@
object, or through get/set methods of the same name (lowercase).
=head1 PARAMETER FOR ALIGNMENT COMPUTATION
-diff --git a/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm b/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
-index 072bb7c..ebdc70d 100755
--- a/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
+++ b/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
@@ -192,7 +192,7 @@ sub new {
@@ -52,8 +48,6 @@
Bio::SimpleAlign).
The nucleotide sequences can be provided as a single filename of a
fasta file containing multiple nucleotide sequences, or an array ref
-diff --git a/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm b/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
-index d874b81..aee27eb 100644
--- a/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
+++ b/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
@@ -117,7 +117,7 @@ Email tqzhang1973 at yahoo.com
@@ -65,8 +59,6 @@
=cut
-diff --git a/lib/Bio/Tools/Run/AssemblerBase.pm b/lib/Bio/Tools/Run/AssemblerBase.pm
-index bd00780..2941470 100644
--- a/lib/Bio/Tools/Run/AssemblerBase.pm
+++ b/lib/Bio/Tools/Run/AssemblerBase.pm
@@ -865,7 +865,7 @@ sub parameters_changed {
@@ -78,11 +70,9 @@
'switches' for boolean program switches
default: all
-diff --git a/lib/Bio/Tools/Run/FootPrinter.pm b/lib/Bio/Tools/Run/FootPrinter.pm
-index 60294f3..dfaa70f 100644
--- a/lib/Bio/Tools/Run/FootPrinter.pm
+++ b/lib/Bio/Tools/Run/FootPrinter.pm
-@@ -67,7 +67,7 @@ Written by Mathieu Blanchette and Martin Tompa. Available here:
+@@ -67,7 +67,7 @@ Written by Mathieu Blanchette and Martin
=head2 Running Footprinter
@@ -91,11 +81,9 @@
FOOTPRINTER_DIR to where the binary is located (even if the executable
is in your path). For example:
-diff --git a/lib/Bio/Tools/Run/Hmmer.pm b/lib/Bio/Tools/Run/Hmmer.pm
-index 9ce3f6e..5abebcc 100755
--- a/lib/Bio/Tools/Run/Hmmer.pm
+++ b/lib/Bio/Tools/Run/Hmmer.pm
-@@ -172,7 +172,7 @@ our @UNSUPPORTED = qw(h verbose a compat pvm);
+@@ -172,7 +172,7 @@ our @UNSUPPORTED = qw(h verbose a
-o is synonymous with -outfile
# may be specified here, allowing run() to be used, or
@@ -104,8 +92,6 @@
# hmmalign()) used later.
-program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch
-diff --git a/lib/Bio/Tools/Run/MCS.pm b/lib/Bio/Tools/Run/MCS.pm
-index af3570b..5924c49 100755
--- a/lib/Bio/Tools/Run/MCS.pm
+++ b/lib/Bio/Tools/Run/MCS.pm
@@ -216,7 +216,7 @@ sub new {
@@ -117,8 +103,6 @@
Bio::SimpleAlign).
The position in the genome can be provided as a Bio::Location::Atomic
-diff --git a/lib/Bio/Tools/Run/Phylo/Gerp.pm b/lib/Bio/Tools/Run/Phylo/Gerp.pm
-index e731b44..9d7c7b5 100755
--- a/lib/Bio/Tools/Run/Phylo/Gerp.pm
+++ b/lib/Bio/Tools/Run/Phylo/Gerp.pm
@@ -211,10 +211,10 @@ sub new {
@@ -134,8 +118,6 @@
In all cases, the alignment sequence names must correspond to node
ids in the tree. Multi-word species names should have the
-diff --git a/lib/Bio/Tools/Run/Phylo/Gumby.pm b/lib/Bio/Tools/Run/Phylo/Gumby.pm
-index 6bfd5ee..bf57965 100644
--- a/lib/Bio/Tools/Run/Phylo/Gumby.pm
+++ b/lib/Bio/Tools/Run/Phylo/Gumby.pm
@@ -284,10 +284,10 @@ sub annots {
@@ -151,8 +133,6 @@
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
-diff --git a/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm b/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
-index bf7f66c..3d59846 100644
--- a/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
+++ b/lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm
@@ -554,7 +554,7 @@ sub set_parameter{
@@ -164,8 +144,6 @@
=cut
-diff --git a/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm b/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
-index 51458f9..0c8ce6b 100644
--- a/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
+++ b/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
@@ -331,13 +331,13 @@ sub rho {
@@ -185,8 +163,6 @@
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
-diff --git a/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm b/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
-index dfd7e4a..940851d 100644
--- a/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
+++ b/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
@@ -241,10 +241,10 @@ sub new {
@@ -202,11 +178,9 @@
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
-diff --git a/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm b/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
-index f68c15b..5aaa208 100644
--- a/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
+++ b/lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm
-@@ -97,7 +97,7 @@ this is still experimental as v3.6 is still under alpha release and not all func
+@@ -97,7 +97,7 @@ this is still experimental as v3.6 is st
Title : TYPE
Description : (optional)
@@ -215,8 +189,6 @@
This program supports 3 types of consensus generation
-diff --git a/lib/Bio/Tools/Run/Phylo/Phyml.pm b/lib/Bio/Tools/Run/Phylo/Phyml.pm
-index 5719281..2004e22 100644
--- a/lib/Bio/Tools/Run/Phylo/Phyml.pm
+++ b/lib/Bio/Tools/Run/Phylo/Phyml.pm
@@ -315,7 +315,7 @@ sub version {
@@ -237,8 +209,6 @@
Returns : string with tree in Newick format, undef before run()
Args : none
-diff --git a/lib/Bio/Tools/Run/Phylo/QuickTree.pm b/lib/Bio/Tools/Run/Phylo/QuickTree.pm
-index 6c61643..909bf1a 100644
--- a/lib/Bio/Tools/Run/Phylo/QuickTree.pm
+++ b/lib/Bio/Tools/Run/Phylo/QuickTree.pm
@@ -240,7 +240,7 @@ sub boot {
@@ -250,8 +220,6 @@
=cut
-diff --git a/lib/Bio/Tools/Run/Phylo/Semphy.pm b/lib/Bio/Tools/Run/Phylo/Semphy.pm
-index 5d155d4..d4faebf 100755
--- a/lib/Bio/Tools/Run/Phylo/Semphy.pm
+++ b/lib/Bio/Tools/Run/Phylo/Semphy.pm
@@ -252,10 +252,10 @@ sub new {
@@ -267,8 +235,6 @@
Bio::DB::Taxonomy object can be supplied, in which case the species
tree will be generated by using the alignment sequence names as
species names and looking for those in the supplied database.
-diff --git a/lib/Bio/Tools/Run/StandAloneBlastPlus.pm b/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
-index 82a2aba..089e7cc 100755
--- a/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
+++ b/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
@@ -210,7 +210,7 @@ To get the tempfile basename, do:
@@ -280,11 +246,9 @@
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-create => 1
-diff --git a/lib/Bio/Tools/Run/TigrAssembler.pm b/lib/Bio/Tools/Run/TigrAssembler.pm
-index 9d76326..757d130 100644
--- a/lib/Bio/Tools/Run/TigrAssembler.pm
+++ b/lib/Bio/Tools/Run/TigrAssembler.pm
-@@ -179,7 +179,7 @@ TIGR Assembler options available in this module:
+@@ -179,7 +179,7 @@ TIGR Assembler options available in this
ignore_tandem_32mers: a flag which causes tandem 32mers (a tandem 32mer is a
32mer which occurs more than once in at least one sequence read) to be
ignored (this is now the default behavior and this flag is for backward
@@ -293,11 +257,9 @@
use_tandem_32mers: a flag which causes tandem 32mers to be used for pairwise
comparison opposite of the -t flag which is now the default).
safe_merging_stop: a flag which causes merging to stop when only sequences
-diff --git a/t/lib/Test/Builder/Tester.pm b/t/lib/Test/Builder/Tester.pm
-index 289bd60..a6380e1 100644
--- a/t/lib/Test/Builder/Tester.pm
+++ b/t/lib/Test/Builder/Tester.pm
-@@ -323,7 +323,7 @@ will function normally and cause success/errors for B<Test::Harness>.
+@@ -323,7 +323,7 @@ will function normally and cause success
sub test_test
{
@@ -306,6 +268,3 @@
my $mess;
my %args;
if (@_ == 1)
---
-1.7.2.5
-
Modified: trunk/packages/bioperl-run/trunk/debian/patches/Use-system-s-Perl.patch
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/patches/Use-system-s-Perl.patch 2013-11-20 21:58:05 UTC (rev 15202)
+++ trunk/packages/bioperl-run/trunk/debian/patches/Use-system-s-Perl.patch 2013-11-20 21:58:35 UTC (rev 15203)
@@ -8,8 +8,6 @@
scripts/bioperl_application_installer.PLS | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
-diff --git a/scripts/bioperl_application_installer.PLS b/scripts/bioperl_application_installer.PLS
-index 6ab5b5e..f4a05c1 100644
--- a/scripts/bioperl_application_installer.PLS
+++ b/scripts/bioperl_application_installer.PLS
@@ -1,4 +1,4 @@
@@ -18,6 +16,3 @@
# BioPerl script for Bio::Installer
#
# Cared for by Albert Vilella
---
-1.7.2.5
-
Modified: trunk/packages/bioperl-run/trunk/debian/patches/install-scripts.patch
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/patches/install-scripts.patch 2013-11-20 21:58:05 UTC (rev 15202)
+++ trunk/packages/bioperl-run/trunk/debian/patches/install-scripts.patch 2013-11-20 21:58:35 UTC (rev 15203)
@@ -8,11 +8,9 @@
Build.PL | 5 +++--
1 files changed, 3 insertions(+), 2 deletions(-)
-diff --git a/Build.PL b/Build.PL
-index a577ecf..531f524 100755
--- a/Build.PL
+++ b/Build.PL
-@@ -28,7 +28,8 @@ my $build = Module::Build->new(
+@@ -27,7 +27,8 @@ my $build = Module::Build->new(
},
get_options => {
accept => { },
@@ -22,15 +20,12 @@
},
auto_features => {
Network => {
-@@ -43,7 +44,7 @@ my $build = Module::Build->new(
+@@ -42,7 +43,7 @@ my $build = Module::Build->new(
my $accept = $build->args->{accept};
# Optionally have script files installed.
-if ($accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
+if ($build->args('install_scripts') or $accept ? 0 : $build->y_n("Install scripts? y/n", 'n')) {
my $files = $build->_find_file_by_type('PLS', 'scripts');
-
+
my $script_build = File::Spec->catdir($build->blib, 'script');
---
-1.7.2.5
-
Modified: trunk/packages/bioperl-run/trunk/debian/rules
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/rules 2013-11-20 21:58:05 UTC (rev 15202)
+++ trunk/packages/bioperl-run/trunk/debian/rules 2013-11-20 21:58:35 UTC (rev 15203)
@@ -5,7 +5,7 @@
endif
%:
- dh $@ --with quilt
+ dh $@
override_dh_auto_configure:
dh_auto_configure -- --install_scripts $(NETWORK)
Added: trunk/packages/bioperl-run/trunk/debian/source/format
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/source/format (rev 0)
+++ trunk/packages/bioperl-run/trunk/debian/source/format 2013-11-20 21:58:35 UTC (rev 15203)
@@ -0,0 +1 @@
+3.0 (quilt)
Modified: trunk/packages/bioperl-run/trunk/debian/watch
===================================================================
--- trunk/packages/bioperl-run/trunk/debian/watch 2013-11-20 21:58:05 UTC (rev 15202)
+++ trunk/packages/bioperl-run/trunk/debian/watch 2013-11-20 21:58:35 UTC (rev 15203)
@@ -1,2 +1,5 @@
version=3
-http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
+opts="uversionmangle=s/_/./g" \
+https://github.com/bioperl/bioperl-run/releases .*/archive/release-(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)$
+
+# http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
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