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)

Dockerfile  view on Meta::CPAN

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

META.json  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",

META.yml  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'
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',



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