Commit 45506cab authored by Andreas Tille's avatar Andreas Tille

Updated version 1.7.1 from 'upstream/1.7.1'

with Debian dir 95ec3fc41a0252f9b57fdfc657438d7844113c3c
parents 29d18ae3 63d590f7
*~
.tmp
*#
.#*
.*.swp
*(Autosaved)blib*
Build
Build.bat
_build*
pm_to_blib*
*.tar.gz
.lwpcookies
cover_db
pod2htm*.tmp
.emacs.*
blib*
*.bak
MYMETA.yml
MYMETA.json
language: perl
perl:
#- "5.24"
- "5.20"
#- "5.18"
- "5.16"
#- "5.14"
sudo: false
env: PERL_CPANM_OPT="--notest --force --skip-satisfied"
addons:
apt:
packages:
- clustalw
- bedtools
- bwa
- ncbi-blast+
- ncbi-blast+-legacy
- muscle
- probcons
- hmmer
- mafft
- emboss
- samtools
- wise
install:
#These are recommended or required Perl libraries
- "cpanm CJFIELDS/BioPerl-1.007000_005.tar.gz 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"
#- "SAMTOOLS=( dirname `which samtools` ) cpanm Bio::DB::Sam 2>&1 | tail -n 1"
script:
- "perl ./Build.PL --accept"
- "./Build test"
#after_success:
# - ./travis_scripts/trigger-dockerhub.sh
#TODO - send emails to bioperl-guts-l
notifications:
email:
recipients:
#- bioperl-guts-l@lists.open-bio.org
- cjfields1@gmail.com
on_success: change
on_failure: change
# whitelist branches
branches:
only:
- master
=head1 CONTRIBUTORS TO BIOPERL-RUN
=over
=item * Sendu Bala <bix at sendu.me.uk>
=item * Jer-Ming Chia <giscjm at nus.edu.sg>
=item * Rob Edwards <redwards at utmem.edu>
=item * Mauricio Herrera Cuadra <mauricio at open-bio.org>
=item * Shawn Hoon <shawnh at fugu-sg.org>
=item * Donald Jackson <donald.jackson at bms.com>
=item * Keith James <kdj at sanger.ac.uk>
=item * Ratnapu Kiran Kumar <kiran at fugu-sg.org>
=item * Balamurugan Kumarasamy <savikalpa at fugu-sg.org>
=item * Catherine Letondal <letondal at pasteur.fr>
=item * Heikki Lehvaslaiho <heikki at ebi.ac.uk>
=item * Stephen Montgomery <smontgom at bcgsc.bc.ca>
=item * Brian Osborne <bosborne at alum.mit.edu>
=item * Tania Oh <gisoht at nus.edu.sg>
=item * Peter Schattner <schattner at alum.mit.edu>
=item * Martin Senger <senger at ebi.ac.uk>
=item * Marc Sohrmann <ms2 at sanger.ac.uk>
=item * Jason Stajich <jason at bioperl.org>
=item * Elia Stupka <elia at fugu-sg.org>
=item * David Vilanova <david.vilanova at urbanet.ch>
=item * Albert Vilella <avilella at gmail.com>
=item * Tiequan Zhang <tqzhang1973 at yahoo.com>
=item * Juguang Xiao <juguang at tll.org.sg>
=back
#!/usr/bin/perl -w
# This is a Module::Build script for BioPerl-Run installation.
# See http://search.cpan.org/~kwilliams/Module-Build/lib/Module/Build.pm
use strict;
use warnings;
use Module::Build;
my $build = Module::Build->subclass(
code => q(
# add dist version to META files
sub get_metadata {
my ($self, %args) = @_;
my $metadata = $self->SUPER::get_metadata(%args);
if (exists $metadata->{provides}) {
my $ver = $self->dist_version;
my $pkgs = $metadata->{provides};
for my $p (keys %{$pkgs}) {
if (!exists($pkgs->{$p}->{'version'})) {
$pkgs->{$p}->{'version'} = $ver;
} else {
$self->log_warn("Note: Module $p has a set version: ".$pkgs->{$p}->{'version'}."\n")
if $pkgs->{$p}->{'version'} ne $ver;
}
}
}
return $metadata;
}
)
)->new(
dist_name => 'BioPerl-Run',
dist_version => '1.007001',
module_name => 'Bio::Run',
dist_author => 'BioPerl Team <bioperl-l@bioperl.org>',
dist_abstract => 'BioPerl-Run - wrapper toolkit',
license => 'perl',
config_requires => {
'Module::Build' => 0,
},
build_requires => {
'Bio::Root::Version' => '1.007000',
'Bio::Root::Test' => 0,
},
requires => {
'perl' => '5.6.1',
'Bio::Root::Version' => '1.007000',
'Bio::Root::Root' => 0,
},
recommends => {
'Algorithm::Diff' => 0, # generating consensus protein family descriptions: Bio::Tools::Run::TribeMCL
'IPC::Run' => 0, # Glimmer and Genemark application wrappers: Bio::Tools::Run::Glimmer Bio::Tools::Run::Genemark
'IO::String' => 0, # generating Bio::Tree::Tree from strings: Bio::Tools::Run::Phylo::Phylip::Consense
'XML::Twig' => 0, # processing XML data: Bio::Tools::Run::EMBOSSacd
'File::Sort' => 0, # BEDTools
'Config::Any' => 0, # MCS, Match
#'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 => {
accept => { },
network => { },
install_scripts => { }
},
auto_features => {
Network => {
description => "Enable tests that need an internet connection",
requires => { 'LWP::UserAgent' => 0 }
}
},
dynamic_config => 1,
#create_makefile_pl => 'passthrough'
);
my $accept = $build->args->{accept};
# Optionally have script files installed.
if ($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');
my @tobp;
while (my ($file, $dest) = each %$files) {
$dest = 'bp_'.File::Basename::basename($dest);
$dest =~ s/PLS$/pl/;
$dest = File::Spec->catfile($script_build, $dest);
$build->copy_if_modified(from => $file, to => $dest);
push @tobp, $dest;
}
$build->script_files(\@tobp);
}
# Do network tests?
my $do_network_tests = 0;
if ($build->args('network')) {
$do_network_tests = $build->feature('Network');
}
elsif ($build->feature('Network')) {
$do_network_tests = $accept ? 0 : $build->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n');
}
if ($do_network_tests) {
$build->notes(network => 1);
$build->log_info(" - will run internet-requiring tests\n");
my $use_email = $build->y_n("Do you want to run tests requiring a valid email address? y/n",'n');
if ($use_email) {
my $address = $build->prompt("Enter email address:");
$build->notes(email => $address);
}
}
else {
$build->notes(network => 0);
$build->log_info(" - will not run internet-requiring tests\n");
}
# Create the build script and exit
$build->create_build_script;
Revision history for bioperl-run modules
1.7.000
* Bio::Tools::Run::WrapperBase moved from bioperl core to bioperl-run
* Updaed Samtools wrapper, minimal support for samtools > v.1 added [cjfields]
* Minor updates to sync with BioPerl v. 1.7.x release series
1.6.901
* added run support for MSAProbs [Jessen Bredeson]
1.6.900
* Bowtie and BWA wrappers for NGS [maj, Ben Bimber, Dan Kortschak]
* ClustalW v2 support [cjfields]
* tRNAscanSE support [Mark Johnson, cjfields]
* Glimmer v2 updates [Mark Johnson, cjfields]
* PAML codeml wrapper updated to work with PAML 4.4d [DaveMessina]
* Phyml updates [hyphaltip]
* Repeatmasker updates [cjfields]
* Initial BLAST+ modules (Bio::Tools::Run::BlastPlus/StandAloneBlastPlus) [maj]
* Improved Bio::Tools::Run::AssemblerBase module and update of the wrappers
that use it [fangly, maj]
* Support for running new de novo and comparative assemblers: 454 Newbler
[fangly], Minimo [fangly], Maq [maj], Samtools [maj], Bowtie [maj]
* [bug 2728] add support to Bio::Tools::Run::Alignment::ClustalW for ClustalW2
[cjfields]
* [RT 50363] make a bit more Windows friendly with file paths
* [bug 2713] - Bio::Tools::Run::Infernal now works with Infernal 1.0 (older
versions deprecated) [cjfields]
* Bio::Tools::Run::Alignment::Gmap added [hartzell]
* [bug 2798] - patch to fix clustalw premature file unlinking error [Wei Zhou]
1.6.0 Release
* All Pise and Pise-related modules and scripts have been moved to the new
bioperl-pise repository. The Pise service is no longer available and has been
replaced by Mobyle. They have been retained as one can still install a Pise
server, and as these modules can possibly be used to create a new BioPerl API
for Mobyle.
1.5.2 Release in sync with bioperl core
* Several wrappers updated for newer versions of the programs.
1.5.1 Release in sync with bioperl core
o First major release in a while, so lots of things in this release
o PHYLIP wrappers are updated for PHYLIP 3.6, some programs will no
longer work (DrawTree and DrawGram specifically) for 3.5 at ths
point. It will depend on whether or not anyone really wants this
if we'll add in the necessary stuf to support 3.5. It isn't
hard, just requires some stuff in th PhylipConf.pm modules.
o Bio::Tools::Run::Alignment::Muscle added
o PAML wrapper for Yn00 and Codeml are more forgiving about the
argument validation.
o Several wrappers updated for newer versions of the programs.
TribeMCL, Genewise, RepeatMasker
1.2.2 Release update in sync with bioperl core
o Soaplab
- API changes
- binary input added
o Pise - changes affecting most Bio::Tools::Run:PiseApplication modules
- Numerous documentation fixes in almost all modules
- Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT
and SEE ALSO parts.
- the DESCRIPTION section now contains *only* the parameters that
can be set by the client.
- remote parameter to -location to conform to
Bio::Tools::Run::AnalysisFactory interface
- new programs sirna, tranalign, twofeat (from EMBOSS 2.6).
o Bio::Tools::Run::Eponine
- More standardized way of running
o Bio::Tools::Run::FootPrinter
- Write the files properly
- Mark Wagner's enhancements bug #1399
o Bio::Tools::Run::Genewise
- more options
o Bio::Tools::Run::Genscan
- doc fix
o Bio::Tools::Run::Hmmpfam
- Updated to set params properly and return a SearchIO object
o Bio::Tools::Run::Mdust
- new location
- Modified to inherit Bio::Tools::Run::WrapperBase
- use Bio::Root::IO to build up paths
- Modified documentation to conform to bioperl format
o Bio::Tools::Run::Signalp
- uniform sequence truncation lenght
o Bio::Tools::Run::Vista
- new module
- Support more options
- More documentation
- fix reverse sequence bug
o Bio::Tools::Run::Phylo::Phylip::SeqBoot
- Allow more than one alignment
o Bio::Tools::Run::Phylo::Phylip::Neighbor
- Check for multiple data sets and set parameter accordingly
o Bio::Tools::Run::Alignment::Blat
- moved from Bio::Tools::Run name space
- some code cleanup to avoid warnings and insure filehandles are
properly closed, etc
o Bio::Tools::Run::Alignment::Lagan
- program name included
- small fixes and addition of options
- added the right credits.
- Bio::Tools::Run::Alignment::DBA and Bio::Tools::Run::Alignment::Sim4
- Quiet declaration warnings
1.2 Developer release
o Analysis Factory framework- currently providing SOAP access to EMBOSS
applications
o Support for FootPrinter, Genewise, Hmmpfam, Primate, Prints,
Profile, Promoterwise, Pseudowise, Seg, Signalp, Tmhmm,TribeMCL,
Blat,DBA,Lagan,Sim4,Fasta,ProtML,Vista
o Added support for PHYLIP apps: Consense, DrawGram, DrawTree, SeqBoot
o Added INSTALL.PROGRAMS providing references to download the program binaries.
o Bug Fixes that hopefully solves the 'too many open files' problem
0.01 Initial release
o Package is broken off from bioperl-live to support just
runnable wrapper modules.
o Support for PAML codeml tested, aaml still waiting
o Support for Molphy protml, nucml to come
o Support for EMBOSS pkg - still need to move component from
bioperl-live Bio::Factory::EMBOSS to this package and
rename it Bio::Tools::Run::EMBOSSFactory or something
equivalent.
o Support for Clustalw, TCoffee, Local NCBI BLAST.
o RepeatMasker, Genscan, Pseudowise, TribeMCL, Primate, Eponine.
o Support for remote analysis through Pise and NCBI Web Blast
queue.
o Select PHYLIP apps: Neighbor, ProtDist, and ProtPars.
BioPerl-run Dependencies
NOTE : This file was auto-generated by the core helper script
maintenance/dependencies.pl. Do not edit directly!
The following packages are used by BioPerl. While not all are required for
BioPerl to operate properly, some functionality will be missing without them.
You can easily choose to install all of these during the normal installation
process. Note that the PPM version of the BioPerl packages always tries to
install all dependencies.
NB: This list of packages is not authoritative. See the 'requires',
'build_requires' and 'recommends' sections of Build.PL instead.
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
| IO-String | * IO::String - IO::File interface | None |
| | for in-core strings | |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::Tools::Run::Phylo::Phylip::Consense - IO::String |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
| IPC-Run | * IPC::Run - Child procs w/ piping, | None |
| | redir and psuedo-ttys | |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::Tools::Run::Genemark - IPC::Run |
| * Bio::Tools::Run::Glimmer - IPC::Run |
| * Bio::Tools::Run::TigrAssembler - IPC::Run |
| * Bio::Tools::Run::tRNAscanSE - IPC::Run |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
| XML-Twig | * XML::Twig - A module for easy | None |
| | processing of XML | |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::Tools::Run::EMBOSSacd - XML::Twig |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
| bioperl | * Bio::Seq - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::Tools::Run::Cap3 - Bio::Seq |
| * Bio::Tools::Run::Genscan - Bio::Seq |
| * 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 |
| * Bio::Tools::Run::Alignment::Muscle - Bio::Seq |
| * Bio::Tools::Run::Alignment::Probalign - Bio::Seq |
| * 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. |
|---------------------------+--------------------------------------+-----------|
| libwww-perl | * HTTP::Request::Common - Functions | None |
| | that generate HTTP::Requests | |
| | * LWP - Libwww-perl | |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::Installer::Generic - HTTP::Request::Common |
| * Bio::Installer::Generic - LWP |
==============================================================================
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.
INSTALLATION
Installation instructions at the following address apply here:
http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix
The next 2 sections summarize the essential points from there.
CPAN INSTALLATION
To install using CPAN you will need a recent version (v1.8802 has
been tested) of it and your prefer_installer conf set to 'MB':
>cpan
cpan>o conf prefer_installer MB
cpan>o conf commit
cpan>q
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
Now install:
cpan>install C/CJ/CJFIELDS/BioPerl-run-1.6.9.tar.gz
If you've installed everything perfectly then you may pass all the tests
run in the './Build test' phase.
It's also possible that you may fail some tests. Possible explanations:
problems with local Perl installation, previously undetected bug in
Bioperl, flawed test script and so on. A few failed tests may not affect
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
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
bioperl-l@bioperl.org.
MANUAL INSTALLATION
Download the bioperl-run archive, then extract its contents. Example:
>gunzip bioperl-run-<release-version>.tar.gz
>tar xvf bioperl-run-<release-version>.tar
>cd bioperl-run
where <release-version> is the current release.
Issue the following command from within bioperl-run/:
>perl Build.PL
You can run regression tests and install bioperl-run using the
following commands:
>./Build test
>./Build install
NOTE: many tests will be skipped without the necessary environment
variables set to tell Bioperl where your programs are installed.
INSTALLING bioperl-run ON WINDOWS
The following page on the BioPerl website has up-to-date
instructions on how to install bioperl-run on Windows:
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