Commit d7bd8646 authored by Andreas Tille's avatar Andreas Tille

Updated version 1.7.2 from 'upstream/1.7.2'

with Debian dir 950a80570e05a8936a518374b89e7a196f176771
parents 0e13d72b cad2ca02
language: perl
perl:
#- "5.24"
- "5.20"
#- "5.18"
- "5.16"
- "5.24"
#- "5.20"
- "5.18"
#- "5.16"
#- "5.14"
sudo: false
......@@ -12,27 +13,33 @@ env: PERL_CPANM_OPT="--notest --force --skip-satisfied"
addons:
apt:
packages:
- clustalw
- bedtools
- bwa
- ncbi-blast+
- ncbi-blast+-legacy
- muscle
- probcons
- clustalw
- bwa
- hmmer
- mafft
- emboss
- samtools
- wise
- probcons
#- emboss
#- wise
#- samtools
#- muscle
#- bedtools
#- mafft
install:
#These are recommended or required Perl libraries
- "cpanm CJFIELDS/BioPerl-1.007000_005.tar.gz 2>&1 | tail -n 1"
- "cpanm Bio::Perl 2>&1 | tail -n 1"
- "cpanm Bio::FeatureIO 2>&1 | tail -n 1"
- "cpanm IPC::Run XML::Twig 2>&1 | tail -n 1"
- "cpanm Config::Any 2>&1 | tail -n 1"
- "cpanm File::Sort 2>&1 | tail -n 1"
#- "SAMTOOLS=( dirname `which samtools` ) cpanm Bio::DB::Sam 2>&1 | tail -n 1"
# Install non-apt dependencies
before_install:
- bash ./packages/install-samtools.sh
- export PATH=$PATH:$HOME/local/bin/
script:
- "perl ./Build.PL --accept"
- "./Build test"
......
......@@ -32,7 +32,7 @@ my $build = Module::Build->subclass(
)
)->new(
dist_name => 'BioPerl-Run',
dist_version => '1.007001',
dist_version => '1.007002',
module_name => 'Bio::Run',
dist_author => 'BioPerl Team <bioperl-l@bioperl.org>',
dist_abstract => 'BioPerl-Run - wrapper toolkit',
......@@ -56,6 +56,7 @@ my $build = Module::Build->subclass(
'XML::Twig' => 0, # processing XML data: Bio::Tools::Run::EMBOSSacd
'File::Sort' => 0, # BEDTools
'Config::Any' => 0, # MCS, Match
'Bio::FeatureIO' => 0, # MCS, Match, Phastcons, Gumby
#'SOAP::Lite' => 0.716, # A bug that affects SoapEU-unit.t tests was fixed in this version (many levels deep object throws error)
},
get_options => {
......
Revision history for bioperl-run modules
1.7.2
* Minor release - PAML, Clustalw, and TCoffee related modules are all
separate distributions, one for each set. These are Bio-Tools-Phylo-PAML,
Bio-Tools-Run-Alignment-TCoffee and Bio-Tools-Run-Alignment-Clustalw
[carandraug]
* Fix EMBOSS and SABlastPlus test count, which was failing when EMBOSS wasn't installed [cjfields]
* Fix various tests to skip if Bio::FeatureIO isn't installed [cjfields]
* Various documentation fixes, including INSTALL updates [bosborne]
* Add Bio::FeatureIO as a 'recommends' (needed for Gumby, MCS, Match, Phastcons)
1.7.001
* Minor release to deal with version indexing
1.7.000
* Bio::Tools::Run::WrapperBase moved from bioperl core to bioperl-run
......
......@@ -57,7 +57,6 @@ NB: This list of packages is not authoritative. See the 'requires',
| * Bio::Tools::Run::TribeMCL - Bio::Seq |
| * Bio::Tools::Run::Vista - Bio::Seq |
| * Bio::Tools::Run::Alignment::Amap - Bio::Seq |
| * Bio::Tools::Run::Alignment::Clustalw - Bio::Seq |
| * Bio::Tools::Run::Alignment::Kalign - Bio::Seq |
| * Bio::Tools::Run::Alignment::Lagan - Bio::Seq |
| * Bio::Tools::Run::Alignment::MAFFT - Bio::Seq |
......@@ -66,7 +65,6 @@ NB: This list of packages is not authoritative. See the 'requires',
| * Bio::Tools::Run::Alignment::Probcons - Bio::Seq |
| * Bio::Tools::Run::Alignment::Proda - Bio::Seq |
| * Bio::Tools::Run::Alignment::StandAloneFasta - Bio::Seq |
| * Bio::Tools::Run::Alignment::TCoffee - Bio::Seq |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
......
......@@ -3,13 +3,13 @@ bioperl-run INSTALLATION
INSTALL THE RIGHT BIOPERL
You need at least the corresponding version of Bioperl. Since this
is BioPerl-run 1.6.9, you should use BioPerl 1.6.9.
is BioPerl-run 1.007001, you should use BioPerl 1.007001.
INSTALLATION
Installation instructions at the following address apply here:
http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
http://bioperl.org/INSTALL.html
The next 2 sections summarize the essential points from there.
......@@ -28,11 +28,11 @@ Find the name of the bioperl-run version you want:
>cpan
cpan>d /bioperl-run/
Database was generated on Mon, 20 Nov 2006 05:24:36 GMT
Distribution C/CJ/CJFIELDS/BioPerl-run-1.6.9.tar.gz
Distribution CJFIELDS/BioPerl-Run-1.007001.tar.gz
Now install:
cpan>install C/CJ/CJFIELDS/BioPerl-run-1.6.9.tar.gz
cpan>install CJFIELDS/BioPerl-Run-1.007001.tar.gz
If you've installed everything perfectly then you may pass all the tests
run in the './Build test' phase.
......@@ -45,7 +45,7 @@ your usage of bioperl-run.
If you decide that the failed tests will not affect how you intend to use
bioperl-run and you'd like to install anyway do:
cpan>force install C/CJ/CJFIELDS/BioPerl-run-1.6.9.tar.gz
cpan>force install CJFIELDS/BioPerl-Run-1.007001.tar.gz
This is what most experienced Bioperl users would do. However, if you're
concerned about a failed test and need assistance or advice then contact
......@@ -68,7 +68,7 @@ Issue the following command from within bioperl-run/:
You can run regression tests and install bioperl-run using the
following commands:
>./Build test
>./Build test
>./Build install
NOTE: many tests will be skipped without the necessary environment
......@@ -83,36 +83,3 @@ http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows
(the instructions are aimed at bioperl-core, but apply
equally to bioperl-run)
ENVIRONMENT VARIABLES
Some important environment variables you need to be aware of.
Variable Values Comment
--------------------------------------------------------------------
PHYLIPVERSION 3.5, 3.6 If you want to run Phylip3.6 you
need to set this env variable to 3.6
BLASTDIR DIR PATH Point to the directory where BLAST
is installed
GENSCAN_DIR DIR PATH Point to the directory where
HumanIso.smat file is installed
EPONINEDIR DIR PATH Point to the directory where
eponine_scan.jar is installed
PAMLDIR DIR PATH Point to directory where PAML is
installed
Generally the all-caps program name concatenated to 'DIR' patten for
environment variable names is followed for most programs. However
there are some exceptions (some require an underscore between the
program name and 'DIR'), so check the documentation for the module
you're interested in using.
Note that for some programs, having the executables in your path is
not enough - the correct environment variable still needs to be set,
and sometimes it shouldn't point to the executable location, but
somewhere else - again, check the documentation.
......@@ -71,10 +71,6 @@ The Bioperl-run package has (Bio)perl wrappers written for the following applica
Bio::Tools::Run::TribeMCL
http://www.ebi.ac.uk/research/cgg/tribe/
18. PAML - Phylogenetic Analysis by Maximum Likelihood package
Bio::Tools::Run::PAML
http://abacus.gene.ucl.ac.uk/software/paml.html
19. Molphy - MOLecular PHYlogenetics Package
Bio::Tools::Run::Molphy
http://www.ism.ac.jp/software/ismlib/softother.e.html
......@@ -83,10 +79,6 @@ The Bioperl-run package has (Bio)perl wrappers written for the following applica
Bio::Tools::Run::Phylip
http://evolution.genetics.washington.edu/phylip.html
21. Clustalw - general purpose multiple sequence alignment program for DNA or proteins
Bio::Tools::Run::Alignment::Clustalw
http://www.ebi.ac.uk/clustalw/
22. DBA - DNA Block Aligner
Bio::Tools::Run::Alignment::DBA
http://www.sanger.ac.uk/software/wise2
......@@ -95,10 +87,6 @@ The Bioperl-run package has (Bio)perl wrappers written for the following applica
Bio::Tools::Run::Alignment::Sim4
http://globin.cse.psu.edu/
24. Tcoffee - Multiple Sequence Alignment Package
Bio::Tools::Run::Alignment::Tcoffee
http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
25. BLAST - Basic Local Alignment Search Tool
Bio::Tools::Run::StandAloneBlast (in bioperl-live CVS repository)
ftp://ftp.ncbi.nih.gov/blast/executables
......
# $Id$
#
# BioPerl module for Bio::Factory::EMBOSS
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Heikki Lehvaslaiho <heikki-at-bioperl-dot-org>
#
......@@ -18,25 +16,24 @@ Bio::Factory::EMBOSS - EMBOSS application factory class
=head1 SYNOPSIS
# get an EMBOSS factory
# Get an EMBOSS factory
use Bio::Factory::EMBOSS;
$f = Bio::Factory::EMBOSS -> new();
# get an EMBOSS application object from the factory
# Get an EMBOSS application object from the factory
$water = $f->program('water') || die "Program not found!\n";
# here is an example of running the application -
# water can compare 1 sequence against 1 or more sequences
# in a database using Smith-Waterman
my $seq_to_test; # this would have a seq here
my @seqs_to_check; # this would be a list of seqs to compare
# (could be just 1)
# Here is an example of running the application - water can
# compare 1 sequence against 1 or more sequences using Smith-Waterman.
# Pass a Sequence object and a reference to an array of objects.
my $wateroutfile = 'out.water';
$water->run({-sequences => $seq_to_test,
-seqall => \@seqs_to_check,
$water->run({-asequence => $seq_object,
-bsequence => \@seq_objects,
-gapopen => '10.0',
-gapextend => '0.5',
-outfile => $wateroutfile});
# now you might want to get the alignment
# Now you might want to get the alignment
use Bio::AlignIO;
my $alnin = Bio::AlignIO->new(-format => 'emboss',
-file => $wateroutfile);
......@@ -69,15 +66,15 @@ Bioperl mailing lists Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
......@@ -138,7 +135,7 @@ sub new {
Function: get/set the location of EMBOSS programs.
Valid values are 'local' and 'novella'.
Returns : string, defaults to 'local'
Args : string
Args : string
=cut
......@@ -269,7 +266,7 @@ sub _program_list {
$self->{'_groups'}->{$groupname} = [] if $groupname;
while ( /^([a-z]\w+) +(.+)$/mg ) {
#print "$1\t$2 \n" if $1;
$self->{'_programs'}->{$1} = $2 if $1;
$self->{'_programs'}->{$1} = $2 if $1;
$self->{'_programgroup'}->{$1} = $groupname if $1;
push @{$self->{'_groups'}->{$groupname}}, $1 if $1;
}
......
# BioPerl module for Bio::Installer::Clustalw
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Albert Vilella
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Installer::Clustalw - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Albert Vilella
Email avilella-AT-gmail-DOT-com
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Installer::Clustalw;
use vars qw(@ISA %DEFAULTS);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Installer::Generic;
@ISA = qw(Bio::Installer::Generic );
BEGIN {
%DEFAULTS = ( 'ORIGIN_DOWNLOAD_DIR' => 'ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw',
'BIN_FOLDER' => '',
'DESTINATION_DOWNLOAD_DIR' => '/tmp',
'DESTINATION_INSTALL_DIR' => "$ENV{'HOME'}",
'PACKAGE_NAME' => 'clustalw1.83.UNIX.tar.gz',
'DIRECTORY_NAME' => 'clustalw1.83',
'ENV_NAME' => 'CLUSTALDIR',
);
}
=head2 get_default
Title : get_default
Usage :
Function:
Example :
Returns :
Args :
=cut
sub get_default {
my $self = shift;
my $param = shift;
return $DEFAULTS{$param};
}
=head2 install
Title : install
Usage : $installer->install();
Function:
Example :
Returns :
Args :
=cut
sub install{
my ($self,@args) = @_;
my $dir;
$self->_decompress;
$self->_execute_make;
$dir = $self->destination_install_dir;
$self->_remember_env;
}
=head2 _execute_make
Title : _execute_make
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _execute_make{
my ($self,@args) = @_;
my $call;
my $destination = $self->destination_install_dir . "/" . $self->directory_name;
print "\n\nCompiling with make -- (this might take a while)\n\n";sleep 1;
if (($^O =~ /dec_osf|linux|unix|bsd|solaris|darwin/i)) {
chdir $destination or die "Cant cd to $destination $!\n";
print "\n\nCalling make (this might take a while)\n\n";sleep 1;
$call = "make";
system("$call") == 0 or $self->throw("Error when trying to run make");
} else {
$self->throw("_execute_make not yet implemented in this platform");
}
}
1;
# BioPerl module for Bio::Installer::PAML
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Albert Vilella
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Installer::PAML - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Albert Vilella
Email avilella-AT-gmail-DOT-com
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Installer::PAML;
use vars qw(@ISA %DEFAULTS);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Installer::Generic;
@ISA = qw(Bio::Installer::Generic );
BEGIN {
%DEFAULTS = ( 'ORIGIN_DOWNLOAD_DIR' => 'http://abacus.gene.ucl.ac.uk/software/',
'BIN_FOLDER' => 'src',
'DESTINATION_DOWNLOAD_DIR' => '/tmp',
'DESTINATION_INSTALL_DIR' => "$ENV{'HOME'}",
'PACKAGE_NAME' => 'paml4a.tar.gz',
'DIRECTORY_NAME' => 'paml4',
'ENV_NAME' => 'PAMLDIR',
);
}
=head2 get_default
Title : get_default
Usage :
Function:
Example :
Returns :
Args :
=cut
sub get_default {
my $self = shift;
my $param = shift;
return $DEFAULTS{$param};
}
=head2 install
Title : install
Usage : $installer->install();
Function:
Example :
Returns :
Args :
=cut
sub install{
my ($self,@args) = @_;
$self->_decompress;
$self->_tweak_paml_makefile;
$self->_execute_paml_makefile;
$self->_remember_env;
}
=head2 _execute_paml_makefile
Title : _execute_paml_makefile
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _execute_paml_makefile{
my ($self,@args) = @_;
my $call;
my $destination = $self->destination_install_dir . "/" . $self->directory_name . "/src";
chdir $destination or $self->throw("Cant cd to $destination");
print "\n\nCompiling now... (this might take a while)\n\n";
if (($^O =~ /dec_osf|linux|unix|bsd|solaris|darwin/i)) {
$call = "make";
system("$call") == 0 or $self->throw("Error when trying to run make");
} else {
$self->throw("_execute_paml_makefile not yet implemented in this platform");
}
}
=head2 _tweak_paml_makefile
Title : _tweak_paml_makefile
Usage :
Function:
Example :
Returns :
Args :
=cut
sub _tweak_paml_makefile{
my ($self,@args) = @_;
my $gcc3;
my $return = qx/gcc -v 2>&1/;
if ($return =~ /version 3/) {
$return = `cat /proc/cpuinfo`;
if( ($return =~ /mmx/) || ($return =~ /3dnow/)) {
my $destination = $self->destination_install_dir . "/" . $self->directory_name . "/src";
chdir $destination or $self->throw("Cant cd to $destination");
my $new = "Makefile";
open(OLD, "< Makefile.UNIX") or $self->throw("can't open Makefile.UNIX");
open(NEW, "> $new") or $self->throw("can't open $new");
while (<OLD>) {
# change $_, then...
$_ =~ s/CFLAGS = -O3/\# CFLAGS = -O3/g;
if( $return =~ /3dnow/ ) {
$_ =~ s/#CFLAGS = -march=athlon -mcpu=athlon -O4 -funroll-loops -fomit-frame-pointer -finline-functions/CFLAGS = -march=athlon -mcpu=athlon -O4 -funroll-loops -fomit-frame-pointer -finline-functions/g;
} elsif( $return =~ /mmx/ ) {
$_ =~ s/#CFLAGS = -march=pentiumpro -mcpu=pentiumpro -O4 -funroll-loops -fomit-frame-pointer -finline-functions/CFLAGS = -march=pentiumpro -mcpu=pentiumpro -O4 -funroll-loops -fomit-frame-pointer -finline-functions/g;
}
print NEW $_ or $self->throw("can't write $new");
}
close(OLD) or $self->throw("can't close Makefile.UNIX");
close(NEW) or $self->throw("can't close $new");
}
}
}
1;
# BioPerl module for Bio::Installer::TCoffee
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Albert Vilella
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Installer::TCoffee - DESCRIPTION of Object
=head1 SYNOPSIS
Give standard usage here
=head1 DESCRIPTION
Describe the object here
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Albert Vilella
Email avilella-AT-gmail-DOT-com
Describe contact details here