Commit 87777eba authored by Andreas Tille's avatar Andreas Tille

Mass commit for 1.6.9-2

parent 5184aaf4
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
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@debian.org> Fri, 15 Nov 2013 10:03:29 +0100
bioperl-run (1.6.9-1) unstable; urgency=low
* New upstream release.
......
Source: bioperl-run
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy@debian.org>,
Andreas Tille <tille@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@lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy@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
Section: perl
Architecture: all
Section: perl
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.
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: *
......
......@@ -26,11 +26,9 @@ Subject: [PATCH] Some spellchecking.
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@bioperl.org.
......@@ -39,8 +37,6 @@ index 2295987..e9afe69 100644
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 @@ index 072bb7c..ebdc70d 100755
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@yahoo.com
......@@ -65,8 +59,6 @@ index d874b81..aee27eb 100644
=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 @@ index bd00780..2941470 100644
'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 @@ index 60294f3..dfaa70f 100644
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 @@ index 9ce3f6e..5abebcc 100755
# 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 @@ index af3570b..5924c49 100755
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 @@ index e731b44..9d7c7b5 100755
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 @@ index 6bfd5ee..bf57965 100644
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 @@ index bf7f66c..3d59846 100644
=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 @@ index 51458f9..0c8ce6b 100644
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 @@ index dfd7e4a..940851d 100644
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 @@ index f68c15b..5aaa208 100644
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 @@ index 5719281..2004e22 100644
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 @@ index 6c61643..909bf1a 100644
=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 @@ index 5d155d4..d4faebf 100755
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 @@ index 82a2aba..089e7cc 100755
$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 @@ index 9d76326..757d130 100644
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 @@ index 289bd60..a6380e1 100644
my $mess;
my %args;
if (@_ == 1)
--
1.7.2.5
......@@ -8,8 +8,6 @@ Subject: [PATCH] Use system's Perl.
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 @@ index 6ab5b5e..f4a05c1 100644
# BioPerl script for Bio::Installer
#
# Cared for by Albert Vilella
--
1.7.2.5
......@@ -8,11 +8,9 @@ Subject: [PATCH] New --install_scripts option to request script installation non
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 @@ index a577ecf..531f524 100755
},
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
......@@ -5,7 +5,7 @@ NETWORK = --network
endif
%:
dh $@ --with quilt
dh $@
override_dh_auto_configure:
dh_auto_configure -- --install_scripts $(NETWORK)
......
version=3
http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
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)$
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment