Bio-Tradis
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CHANGELOG.md view on Meta::CPAN
## [1.4.1](https://github.com/sanger-pathogens/Bio-Tradis/tree/1.4.1) (2018-07-19)
[Full Changelog](https://github.com/sanger-pathogens/Bio-Tradis/compare/1.4.0...1.4.1)
**Closed issues:**
- Installation on Ubuntu 17.10 fails [\#84](https://github.com/sanger-pathogens/Bio-Tradis/issues/84)
- Port 18 volume discrepancy? [\#83](https://github.com/sanger-pathogens/Bio-Tradis/issues/83)
**Merged pull requests:**
- Change TryCatch to Try::Tiny [\#94](https://github.com/sanger-pathogens/Bio-Tradis/pull/94) ([ssjunnebo](https://github.com/ssjunnebo))
- fix typo in badge [\#93](https://github.com/sanger-pathogens/Bio-Tradis/pull/93) ([ssjunnebo](https://github.com/ssjunnebo))
- Include TOC [\#92](https://github.com/sanger-pathogens/Bio-Tradis/pull/92) ([ssjunnebo](https://github.com/ssjunnebo))
- 621538 docker [\#91](https://github.com/sanger-pathogens/Bio-Tradis/pull/91) ([ssjunnebo](https://github.com/ssjunnebo))
- 621538 docker [\#90](https://github.com/sanger-pathogens/Bio-Tradis/pull/90) ([ssjunnebo](https://github.com/ssjunnebo))
- include reference genome for cram [\#89](https://github.com/sanger-pathogens/Bio-Tradis/pull/89) ([ssjunnebo](https://github.com/ssjunnebo))
- Revert "Replace cram file without reads" [\#88](https://github.com/sanger-pathogens/Bio-Tradis/pull/88) ([ssjunnebo](https://github.com/ssjunnebo))
- Replace cram file without reads [\#87](https://github.com/sanger-pathogens/Bio-Tradis/pull/87) ([ssjunnebo](https://github.com/ssjunnebo))
- update tutorial for ENA switch to https \(from http\) [\#85](https://github.com/sanger-pathogens/Bio-Tradis/pull/85) ([lbarquist](https://github.com/lbarquist))
## [1.4.0](https://github.com/sanger-pathogens/Bio-Tradis/tree/1.4.0) (2017-11-28)
RUN apt-get update -qq && apt-get install -y sudo make wget unzip zlib1g-dev cpanminus gcc bzip2 libncurses5-dev libncursesw5-dev libssl-dev r-base git libxml-libxml-perl libgd-gd2-perl bioperl bwa smalt tabix samtools
RUN wget https://github.com/lh3/minimap2/releases/download/v2.17/minimap2-2.17_x64-linux.tar.bz2
RUN tar xjfv minimap2-2.17_x64-linux.tar.bz2
# Install R dependencies
RUN Rscript -e "install.packages('BiocManager')" -e "BiocManager::install()" -e "BiocManager::install(c('edgeR','getopt', 'MASS'))"
# Install some perl dependencies (will probably install more later after adding source code).
# It seems like we have to force installation of Xpath because the tests fail for some reason.
# This in turn means we need to force install BioPerl as well
RUN cpanm IPC::System::Simple DateTime::Locale DateTime Dist::Zilla Moose Text::CSV ExtUtils::MakeMaker Getopt::Long Try::Tiny Exception::Class
RUN cpanm Dist::Zilla::Plugin::AutoPrereqs Dist::Zilla::Plugin::Encoding Dist::Zilla::Plugin::FileFinder::ByName Dist::Zilla::Plugin::MetaResources Dist::Zilla::Plugin::PkgVersion Dist::Zilla::Plugin::PodWeaver Dist::Zilla::Plugin::RequiresExternal D...
RUN cpanm --force XML::DOM::XPath
RUN cpanm --force Bio::Seq Bio::SeqIO
# Add source code
ADD . Bio-Tradis
# Install missing dependencies gathered from source code
# This can take a while and slow down building the docker image if we install everything this way.
# Some known dependencies are installed earlier in the dockerfile (before adding source code) to speed up build time
"Data::Dumper" : "0",
"Exception::Class" : "0",
"File::Basename" : "0",
"File::Path" : "0",
"File::Spec" : "0",
"File::Temp" : "0",
"FindBin" : "0",
"Getopt::Long" : "0",
"Moose" : "0",
"Text::CSV" : "0",
"Try::Tiny" : "0",
"strict" : "0",
"warnings" : "0"
}
},
"test" : {
"recommends" : {
"CPAN::Meta" : "2.120900"
},
"requires" : {
"Env::Path" : "0.18",
Data::Dumper: '0'
Exception::Class: '0'
File::Basename: '0'
File::Path: '0'
File::Spec: '0'
File::Temp: '0'
FindBin: '0'
Getopt::Long: '0'
Moose: '0'
Text::CSV: '0'
Try::Tiny: '0'
strict: '0'
warnings: '0'
resources:
homepage: http://www.sanger.ac.uk/
repository: https://github.com/sanger-pathogens/Bio-Tradis.git
version: 1.4.5
x_Dist_Zilla:
perl:
version: '5.030000'
plugins:
Makefile.PL view on Meta::CPAN
"Data::Dumper" => 0,
"Exception::Class" => 0,
"File::Basename" => 0,
"File::Path" => 0,
"File::Spec" => 0,
"File::Temp" => 0,
"FindBin" => 0,
"Getopt::Long" => 0,
"Moose" => 0,
"Text::CSV" => 0,
"Try::Tiny" => 0,
"strict" => 0,
"warnings" => 0
},
"TEST_REQUIRES" => {
"Env::Path" => "0.18",
"ExtUtils::MakeMaker" => 0,
"File::Spec" => 0,
"Test::Exception" => 0,
"Test::Files" => 0,
"Test::More" => 0,
Makefile.PL view on Meta::CPAN
"File::Spec" => 0,
"File::Temp" => 0,
"FindBin" => 0,
"Getopt::Long" => 0,
"Moose" => 0,
"Test::Exception" => 0,
"Test::Files" => 0,
"Test::More" => 0,
"Test::Most" => 0,
"Text::CSV" => 0,
"Try::Tiny" => 0,
"strict" => 0,
"warnings" => 0
);
unless ( eval { ExtUtils::MakeMaker->VERSION(6.63_03) } ) {
delete $WriteMakefileArgs{TEST_REQUIRES};
delete $WriteMakefileArgs{BUILD_REQUIRES};
$WriteMakefileArgs{PREREQ_PM} = \%FallbackPrereqs;
}
lib/Bio/Tradis/CommandLine/TradisAnalysis.pm view on Meta::CPAN
package Bio::Tradis::CommandLine::TradisAnalysis;
$Bio::Tradis::CommandLine::TradisAnalysis::VERSION = '1.4.5';
# ABSTRACT: Perform full tradis analysis
use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd qw(abs_path cwd);
use Bio::Tradis::RunTradis;
use Try::Tiny;
has 'args' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str', required => 1 );
has 'fastqfile' => ( is => 'rw', isa => 'Str', required => 0 );
has 'tag' => ( is => 'rw', isa => 'Maybe[Str]', required => 0 );
has 'mismatch' => ( is => 'rw', isa => 'Int', required => 0, default => 0 );
has 'tagdirection' =>
( is => 'rw', isa => 'Str', required => 0, default => '3' );
has 'reference' => ( is => 'rw', isa => 'Str', required => 0 );
has 'help' => ( is => 'rw', isa => 'Bool', required => 0 );
t/00-report-prereqs.dd view on Meta::CPAN
'Data::Dumper' => '0',
'Exception::Class' => '0',
'File::Basename' => '0',
'File::Path' => '0',
'File::Spec' => '0',
'File::Temp' => '0',
'FindBin' => '0',
'Getopt::Long' => '0',
'Moose' => '0',
'Text::CSV' => '0',
'Try::Tiny' => '0',
'strict' => '0',
'warnings' => '0'
}
},
'test' => {
'recommends' => {
'CPAN::Meta' => '2.120900'
},
'requires' => {
'Env::Path' => '0.18',
( run in 1.658 second using v1.01-cache-2.11-cpan-05444aca049 )