Commit f0a273ea authored by Andreas Tille's avatar Andreas Tille

New upstream version

parent 8234880f
bioperl-run (1.6.9-4) UNRELEASED; urgency=medium
bioperl-run (1.7.1-1) UNRELEASED; urgency=medium
* New upstream version
* Testsuite: autopkgtest-pkg-perl
* cme fix dpkg-control
* Enable lots of tests
......@@ -7,6 +8,9 @@ bioperl-run (1.6.9-4) UNRELEASED; urgency=medium
bioperl-run in commit acd57a7d14112c5fd2cd979005b072efdaf57679 which is
taken over in quilt patch
* Fix homepage
* d/watch:
- version=4
- Fix versionmangling
-- Andreas Tille <tille@debian.org> Fri, 16 Dec 2016 09:17:37 +0100
......
Forwarded: https://redmine.open-bio.org/issues/3256
From b6c1d10797c2fbb6c5fe3c0fe2e5f74d252889cb Mon Sep 17 00:00:00 2001
From: Charles Plessy <plessy@debian.org>
Date: Sat, 18 Jun 2011 13:13:43 +0900
Subject: [PATCH] Some spellchecking.
---
lib/Bio/Tools/Run/Alignment/Clustalw.pm | 2 +-
lib/Bio/Tools/Run/Alignment/Pal2Nal.pm | 2 +-
lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm | 2 +-
lib/Bio/Tools/Run/AssemblerBase.pm | 2 +-
lib/Bio/Tools/Run/FootPrinter.pm | 2 +-
lib/Bio/Tools/Run/Hmmer.pm | 2 +-
lib/Bio/Tools/Run/MCS.pm | 2 +-
lib/Bio/Tools/Run/Phylo/Gerp.pm | 4 ++--
lib/Bio/Tools/Run/Phylo/Gumby.pm | 4 ++--
lib/Bio/Tools/Run/Phylo/PAML/Baseml.pm | 2 +-
lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm | 6 +++---
lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm | 4 ++--
lib/Bio/Tools/Run/Phylo/Phylip/Consense.pm | 2 +-
lib/Bio/Tools/Run/Phylo/Phyml.pm | 4 ++--
lib/Bio/Tools/Run/Phylo/QuickTree.pm | 2 +-
lib/Bio/Tools/Run/Phylo/Semphy.pm | 4 ++--
lib/Bio/Tools/Run/StandAloneBlastPlus.pm | 2 +-
lib/Bio/Tools/Run/TigrAssembler.pm | 2 +-
t/lib/Test/Builder/Tester.pm | 2 +-
19 files changed, 26 insertions(+), 26 deletions(-)
--- 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 imple
that a specific clustalw feature be added to this perl contact
bioperl-l@bioperl.org.
-These can be specified as paramters when instantiating a new Clustalw
+These can be specified as parameters when instantiating a new Clustalw
object, or through get/set methods of the same name (lowercase).
=head1 PARAMETER FOR ALIGNMENT COMPUTATION
--- a/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
+++ b/lib/Bio/Tools/Run/Alignment/Pal2Nal.pm
@@ -192,7 +192,7 @@ sub new {
Args : The first argument represents a protein alignment, the second
argument a set of nucleotide sequences.
The alignment can be provided as an alignment file readable by
- Bio::AlignIO, or a Bio::Align::AlignI complient object (eg. a
+ Bio::AlignIO, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The nucleotide sequences can be provided as a single filename of a
fasta file containing multiple nucleotide sequences, or an array ref
--- a/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
+++ b/lib/Bio/Tools/Run/Alignment/StandAloneFasta.pm
@@ -117,7 +117,7 @@ Email tqzhang1973@yahoo.com
=head1 Appendix
The rest of the documendation details each of the object
-methods. Internal methods are preceeded with a underscore
+methods. Internal methods are preceded with a underscore
=cut
--- a/lib/Bio/Tools/Run/AssemblerBase.pm
+++ b/lib/Bio/Tools/Run/AssemblerBase.pm
@@ -865,7 +865,7 @@ sub parameters_changed {
Usage : @params = $pobj->available_parameters()
Function: Returns a list of the available parameters
Returns : Array of parameters
- Args : 'params' for settable program paramters
+ Args : 'params' for settable program parameters
'switches' for boolean program switches
default: all
--- a/lib/Bio/Tools/Run/FootPrinter.pm
+++ b/lib/Bio/Tools/Run/FootPrinter.pm
@@ -67,7 +67,7 @@ Written by Mathieu Blanchette and Martin
=head2 Running Footprinter
-To run FootPrinter, you will need to set the enviroment variable
+To run FootPrinter, you will need to set the environment variable
FOOTPRINTER_DIR to where the binary is located (even if the executable
is in your path). For example:
--- a/lib/Bio/Tools/Run/Hmmer.pm
+++ b/lib/Bio/Tools/Run/Hmmer.pm
@@ -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
- # it can be ommitted and the corresponding method (eg.
+ # it can be omitted and the corresponding method (eg.
# hmmalign()) used later.
-program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch
--- a/lib/Bio/Tools/Run/MCS.pm
+++ b/lib/Bio/Tools/Run/MCS.pm
@@ -216,7 +216,7 @@ sub new {
third argument represents annotation of the exons in the alignment.
The alignment can be provided as a multi-fasta format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The position in the genome can be provided as a Bio::Location::Atomic
--- a/lib/Bio/Tools/Run/Phylo/Gerp.pm
+++ b/lib/Bio/Tools/Run/Phylo/Gerp.pm
@@ -211,10 +211,10 @@ sub new {
Args : The first argument represents an alignment, the second argument
a phylogenetic tree with branch lengths.
The alignment can be provided as a MAF format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
- or a Bio::Tree::TreeI complient object.
+ or a Bio::Tree::TreeI compliant object.
In all cases, the alignment sequence names must correspond to node
ids in the tree. Multi-word species names should have the
--- a/lib/Bio/Tools/Run/Phylo/Gumby.pm
+++ b/lib/Bio/Tools/Run/Phylo/Gumby.pm
@@ -284,10 +284,10 @@ sub annots {
Args : The first argument represents an alignment, the second argument
a species tree.
The alignment can be provided as a multi-fasta format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
- or a Bio::Tree::TreeI complient object. Alternatively a
+ or a Bio::Tree::TreeI compliant object. Alternatively a
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.
--- 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{
Returns : none
Args : boolean: keep existing parameter values
NB : using this isn't an especially good idea! You don't need to do
- anything to end up using default paramters: hence 'default'!
+ anything to end up using default parameters: hence 'default'!
=cut
--- a/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
+++ b/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm
@@ -331,13 +331,13 @@ sub rho {
('footprinting').
Returns : array of Bio::SeqFeature::Annotated (one feature per alignment
sequence and prediction)
- Args : The first arguement represents an alignment, the second arguement
+ Args : The first argument represents an alignment, the second argument
a species tree.
The alignment can be provided as a multi-fasta format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
- or a Bio::Tree::TreeI complient object. Alternatively a
+ or a Bio::Tree::TreeI compliant object. Alternatively a
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.
--- a/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
+++ b/lib/Bio/Tools/Run/Phylo/Phast/PhyloFit.pm
@@ -241,10 +241,10 @@ sub new {
Args : The first argument represents an alignment, the second argument
a species tree.
The alignment can be provided as a multi-fasta format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
- or a Bio::Tree::TreeI complient object. Alternatively a
+ or a Bio::Tree::TreeI compliant object. Alternatively a
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.
--- 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 st
Title : TYPE
Description : (optional)
- Only avaliable in phylip v3.6
+ Only available in phylip v3.6
This program supports 3 types of consensus generation
--- a/lib/Bio/Tools/Run/Phylo/Phyml.pm
+++ b/lib/Bio/Tools/Run/Phylo/Phyml.pm
@@ -315,7 +315,7 @@ sub version {
Returns : Bio::Tree::Tree object
Args : file name for your input alignment in a format
recognised by AlignIO, OR Bio::Align::AlignI
- complient object (eg. Bio::SimpleAlign).
+ compliant object (eg. Bio::SimpleAlign).
=cut
@@ -358,7 +358,7 @@ sub stats {
Title : tree_string
Usage : $factory->tree_string;
$factory->run($align_object);
- Function: Returns the contents of the phyml '_phyml_tree.txt' ouput file
+ Function: Returns the contents of the phyml '_phyml_tree.txt' output file
Returns : string with tree in Newick format, undef before run()
Args : none
--- a/lib/Bio/Tools/Run/Phylo/QuickTree.pm
+++ b/lib/Bio/Tools/Run/Phylo/QuickTree.pm
@@ -240,7 +240,7 @@ sub boot {
Function: Runs QuickTree to generate a tree
Returns : Bio::Tree::Tree object
Args : file name for your input alignment in stockholm format, OR
- Bio::Align::AlignI complient object (eg. Bio::SimpleAlign).
+ Bio::Align::AlignI compliant object (eg. Bio::SimpleAlign).
=cut
--- a/lib/Bio/Tools/Run/Phylo/Semphy.pm
+++ b/lib/Bio/Tools/Run/Phylo/Semphy.pm
@@ -252,10 +252,10 @@ sub new {
argument a species tree (to set an initial tree: normally the -t
option to Semphy).
The alignment can be provided as a multi-fasta format alignment
- filename, or a Bio::Align::AlignI complient object (eg. a
+ filename, or a Bio::Align::AlignI compliant object (eg. a
Bio::SimpleAlign).
The species tree can be provided as a newick format tree filename
- or a Bio::Tree::TreeI complient object. Alternatively a
+ or a Bio::Tree::TreeI compliant object. Alternatively a
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.
--- a/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
+++ b/lib/Bio/Tools/Run/StandAloneBlastPlus.pm
@@ -210,7 +210,7 @@ To get the tempfile basename, do:
=item * Specify data post-construction
-Use the explict attribute setters:
+Use the explicit attribute setters:
$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-create => 1
--- a/lib/Bio/Tools/Run/TigrAssembler.pm
+++ b/lib/Bio/Tools/Run/TigrAssembler.pm
@@ -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
- compatability)
+ compatibility)
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
--- a/t/lib/Test/Builder/Tester.pm
+++ b/t/lib/Test/Builder/Tester.pm
@@ -323,7 +323,7 @@ will function normally and cause success
sub test_test
{
- # decode the arguements as described in the pod
+ # decode the arguments as described in the pod
my $mess;
my %args;
if (@_ == 1)
Forwarded: https://redmine.open-bio.org/issues/3255
From 8d4322bea521c457029a00155fe292ef7ef177d4 Mon Sep 17 00:00:00 2001
From: Charles Plessy <plessy@debian.org>
Date: Sat, 18 Jun 2011 12:58:08 +0900
Subject: [PATCH] Use system's Perl.
---
scripts/bioperl_application_installer.PLS | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
--- a/scripts/bioperl_application_installer.PLS
+++ b/scripts/bioperl_application_installer.PLS
@@ -1,4 +1,4 @@
-#!/usr/local/bin/perl
+#!/usr/bin/perl
# BioPerl script for Bio::Installer
#
# Cared for by Albert Vilella
Forwarded: https://redmine.open-bio.org/issues/3254
From 4d1fe98b390c67170d0d23325de5ccd8fdc6ea1a Mon Sep 17 00:00:00 2001
From: Charles Plessy <plessy@debian.org>
Date: Sat, 18 Jun 2011 12:43:21 +0900
Subject: [PATCH] New --install_scripts option to request script installation non-interactively.
---
Build.PL | 5 +++--
1 files changed, 3 insertions(+), 2 deletions(-)
--- a/Build.PL
+++ b/Build.PL
@@ -27,7 +27,8 @@ my $build = Module::Build->new(
},
get_options => {
accept => { },
- network => { }
+ network => { },
+ install_scripts => { }
},
auto_features => {
Network => {
@@ -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');
This source diff could not be displayed because it is too large. You can view the blob instead.
install-scripts.patch
Use-system-s-Perl.patch
Some-spellchecking.patch
move-StandAloneBlast-and-WrapperBase-from-root-Bio.-.patch
skip_tests_for_wise.patch
skip_tests_for_muscle.patch
# skip_tests_for_bowtie.patch
# skip_tests_for_muscle.patch # does not apply in 1.7.1
# skip_tests_for_bowtie.patch # skip whole patch in 1.6.9
skip_tests_for_phylip.patch
# skip_tests_for_infernal.patch
# skip_tests_for_infernal.patch # skip whole patch in 1.6.9
skip_tests_for_phyml.patch
skip_tests_for_ncbi-blast+.patch
skip_tests_for_samtools.patch
# skip_tests_for_ncbi-blast+.patch # does not apply in 1.7.1
# skip_tests_for_samtools.patch # does not apply in 1.7.1
skip_tests_for_t-coffee.patch
skip_tests_for_maq.patch
# skip_tests_for_maq.patch # does not apply in 1.7.1
......@@ -2,40 +2,9 @@ Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 16 Dec 2016 09:17:37 +0100
Description: No idea why the number of tests is 8 instead of 9
--- a/t/Consense.t
+++ b/t/Consense.t
@@ -6,7 +6,7 @@ use strict;
BEGIN {
use Bio::Root::Test;
- test_begin(-tests => 9,
+ test_begin(-tests => 8,
-requires_module => 'IO::String');
use_ok('Bio::Tools::Run::Phylo::Phylip::Consense');
use_ok('Bio::AlignIO');
--- a/t/Neighbor.t
+++ b/t/Neighbor.t
@@ -103,10 +103,10 @@ SKIP: {
@nodes = sort { defined $a->id &&
defined $b->id &&
$a->id cmp $b->id } $tree->get_nodes();
- is ($nodes[12]->id, 'S01',"failed to assign serial names");
- foreach my $nd (@nodes){
- $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
- }
- is ($nodes[12]->id, 'Spar_21273',"failed to restore original names");
+ #is ($nodes[12]->id, 'S01',"failed to assign serial names"); # Got undef in these tests! FIXME
+ #foreach my $nd (@nodes){
+ # $nd->id($ref_name->{$nd->id_output}) if $nd->is_Leaf;
+ #}
+ #is ($nodes[12]->id, 'Spar_21273',"failed to restore original names");
-}
\ No newline at end of file
+}
--- a/t/ProtPars.t
+++ b/t/ProtPars.t
@@ -8,7 +8,7 @@ $DEBUG = test_debug();
@@ -7,7 +7,7 @@ $DEBUG = test_debug();
use strict;
BEGIN {
use Bio::Root::Test;
......@@ -44,8 +13,8 @@ Description: No idea why the number of tests is 8 instead of 9
use_ok('Bio::Tools::Run::Phylo::Phylip::ProtPars');
use_ok('Bio::Tools::Run::Alignment::Clustalw');
}
@@ -81,10 +81,10 @@ SKIP: {
@nodes = sort { $a->id cmp $b->id } $tree->get_nodes();
@@ -78,10 +78,10 @@ SKIP: {
@nodes = sort { $a->id cmp $b->id } $tree2->get_nodes();
is (scalar(@nodes),27,
"creating tree by protpars");
- is ($nodes[12]->id, 'S01',"assign serial names");
......
......@@ -40,25 +40,7 @@ Description: Somehow there are issues to initialise openmpi, but beside these wa
--- a/t/Phyml.t
+++ b/t/Phyml.t
@@ -5,7 +5,7 @@ use strict;
BEGIN {
use Bio::Root::Test;
- test_begin(-tests => 47);
+ test_begin(-tests => 42);
use_ok('Bio::Tools::Run::Phylo::Phyml');
use_ok('Bio::AlignIO');
}
@@ -88,7 +88,7 @@ SKIP: {
is ($factory->data_type('dna'), '0', 'data_type, dna');
is ($factory->data_type('protein'), '1', 'data_type, protein');
- is ($factory->model, 'JTT', 'model, default');
+ # is ($factory->model, 'JTT', 'model, default'); # got: 'WAG' - expected: 'JTT'
is ($factory->opt_topology, 'y', 'opt_topology, default');
@@ -106,18 +106,17 @@ SKIP: {
@@ -103,18 +103,17 @@ SKIP: {
# $factory->tempdir($workdir);
# using filename input
......@@ -87,7 +69,7 @@ Description: Somehow there are issues to initialise openmpi, but beside these wa
# using AlignIO on a DNA MSA
@@ -148,8 +147,8 @@ SKIP: {
@@ -145,7 +144,7 @@ SKIP: {
$factory = Bio::Tools::Run::Phylo::Phyml->new(%args);
$factory->save_tempfiles(1);
......@@ -98,4 +80,3 @@ Description: Somehow there are issues to initialise openmpi, but beside these wa
+ #@leaves = $tree->get_leaf_nodes;
+ #is (@leaves, 5, 'Result tree from DNA SimpleAlign input had correct number of leaves');
}
......@@ -7,19 +7,16 @@ endif
# The following programs are not packaged for Debian and thus
# the test is not supported
NOT_SUPPORTED_TESTS=Blat \
Bowtie \
Eponine \
Glimmer2 \
Gumby \
Infernal \
RepeatMasker
# Cap3 - some sensible tests seem to run despite this is not packaged
# The following tests should work but are missing to be packaged BioPerl modules
FAILING_TESTS_FOR_DUE_TO_MISSING_MODULES=BWA \
MCS \
Match
MCS
%:
dh $@
......
version=3
opts="uversionmangle=s/_/./g" \
version=4
opts="uversionmangle=s/[-_]/./g" \
https://github.com/bioperl/bioperl-run/releases .*/archive/release-(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)$
# http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
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