Perl - modules

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Description

Perl programming language supports extensions in the form of so called 'modules'. To ease the administration of such modules we grouped them into one SW package (module). These packages are dependent on the Perl.

Availability

Freely available to all MetaCentrum users. Versions 1.6.1 a 1.6.9-gcc Module list:

Module name Included Perl modules
bioperl-1.6.1 Ace (1.92), Acme::Damn (0.05), Algorithm::Munkres (0.08), App::cpanminus (1.7001), Archive::Zip (1.37), Array::Compare (2.02), BerkeleyDB (0.54), Bio (), Bio::Run (), Bit::Vector (7.3), CPAN::DistnameInfo (0.12), CPAN::Meta (2.140640), CPAN::Meta::Check (0.008), CPAN::Meta::Requirements (2.125), CPAN::Meta::YAML (0.012), Cache::Cache (1.06), Canary::Stability (), Carp::Clan (6.04), Class::Data::Inheritable (0.08), Class::Load (0.20), Clone (0.35), Convert::Binary::C (0.76), Crypt::RC4 (2.02), DBD::SQLite (1.40), Data (), Data::OptList (0.108), Devel::GlobalDestruction (0.12), Devel::GlobalDestruction::XS (0.01), Devel::StackTrace (1.30), Digest::Perl::MD5 (1.8), Dist::CheckConflicts (0.09), Eval::Closure (0.11), Exception::Class (1.37), File::Slurp (9999.19), File::Which (1.09), Graph (0.96), IO::All (0.51), IO::Prompt (0.997002), IPC::Run3 (0.046), IPC::System::Simple (1.25), Inline (0.53), JSON (2.61), JSON::PP (2.27203), List::MoreUtils (0.33), MRO::Compat (0.12), Math::Derivative (undef), Math::Random (0.71), Math::Spline (0.02), Module::Implementation (0.07), Module::Metadata (1.000019), Module::Runtime (0.013), Moose (2.1005), OLE::Storage_Lite (0.19), PPM (undef), Package::DeprecationManager (0.13), Package::Stash (0.36), Package::Stash::XS (0.28), Params::Util (1.07), Perl (5.20.2), Perl::OSType (1.007), Perl::Unsafe::Signals (0.02), PerlIO::gzip (0.18), PostScript::Metrics (0.06), Probe::Perl (0.03), Proc::ProcessTable (0.50), SVG (2.59), SVG::Graph (0.02), Set::Scalar (1.26), Spreadsheet::ParseExcel (0.59), Spreadsheet::WriteExcel (2.40), Statistics::Descriptive (3.0605), Sub::Exporter (0.987), Sub::Exporter::Progressive (0.001011), Sub::Install (0.927), Sub::Name (0.05), Sub::Uplevel (0.24), Sys::SigAction (0.21), Term::ReadKey (2.31), Test::CheckDeps (0.010), Test::Deep (0.110), Test::Differences (0.61), Test::Exception (0.32), Test::Fatal (0.013), Test::Most (0.31), Test::NoWarnings (1.04), Test::Requires (0.06), Test::Script (1.07), Test::Warn (0.24), Text::Diff (1.41), Text::Soundex (3.04), Tree::DAG_Node (1.18), Try::Tiny (0.18), Want (0.22), XML::DOM::XPath (0.14), XML::Filter::BufferText (1.01), XML::SAX::Writer (0.53), XML::Twig (3.44), XML::Writer (0.623), XML::XPathEngine (0.14), YAML (0.81), YAML::Syck (1.25), bin::pairfq (), forks (0.34)
bioperl-1.6.9-gcc Algorithm::Diff (1.1903), Archive::Tar (2.04), Archive::Zip (1.45), Bio (), Bio::SamTools (), CPAN (2.16), CPAN::Meta (2.143240), Capture::Tiny (0.28), Carp (1.38), Class::Data::Inheritable (0.08), Clone (0.37), Compress::Raw::Bzip2 (2.064), Compress::Raw::Zlib (2.065), Config::General (2.63), Crypt::Blowfish (), Crypt::CBC (2.33), Cwd (3.48_01), Data (), Data::Dumper (2.151_01), Devel::StackTrace (2.00), Digest::MD5 (2.53), Digest::SHA (5.88), Exception::Class (1.39), Exporter::Tiny (0.042), ExtUtils::CBuilder (0.280220), ExtUtils::Config (0.008), ExtUtils::Helpers (0.026), ExtUtils::InstallPaths (0.011), ExtUtils::MakeMaker (7.04), File::HomeDir (1.00), File::Slurp (9999.19), File::Which (1.19), Filesys::Df (), Font::TTF (1.06), GD (), Getopt::Long (2.49), IO::Socket::SSL (2.019), IO::String (1.08), IPC::Run3 (0.048), JSON (2.90), JSON::PP (2.27400), List::MoreUtils (0.33), List::Util (1.38), Log::Log4perl (1.46), Math::Bezier (0.01), Math::Round (0.07), Math::VecStat (0.08), Module::Build (0.4220), Module::Build::Tiny (0.039), Module::Implementation (0.09), Module::Runtime (0.014), Mozilla::CA (20150826), Net (), Net::SSLeay (1.65), Number::Format (1.75), Params::Validate (), Perl (5.20.2), Pod (), Pod::Usage (1.69), Probe::Perl (0.03), Readonly (2.05), Regexp::Common (2016060801), SVG (2.64), Set::IntSpan (1.19), Socket (2.013), Spiffy (0.46), Statistics::Basic (1.6611), Storable (2.49_01), Sub::Uplevel (0.25), Term::ReadKey (2.32), Term::ReadLine (1.14), Test::Deep (0.115), Test::Differences (0.63), Test::Exception (0.38), Test::Fatal (0.014), Test::Harness (3.35), Test::Most (0.34), Test::NoWarnings (1.04), Test::Requires (0.10), Test::Simple (1.001014), Test::Warn (0.30), Text::Balanced (2.03), Text::Diff (1.41), Text::Format (0.60), Text::Glob (0.09), Time::HiRes (1.9726), Try::Tiny (0.28), URI (1.67), XSLoader (0.17)

Licence

Differs according to used Perl module.

Use

Initialize environment with command:

module add bioperl-1.6.1

or

module add bioperl-1.6.9-gcc

You can also install your own Perl module, see SW installation for details.

To list all available perl modules you can use script perl_installed_modules.pl. Usage:

module add bioperl-1.6.1
perl_installed_modules.pl
Note: If you want to check a list of available modules for bioperl-1.6.1, is necessary replace default perl-5.10.1 by newest version e.g. perl-5.20.1-gcc. Use module rm and module add commands.
module add bioperl-1.6.9-gcc
perl_installed_modules.pl

Documentation

Perl modules documentation is available through CPAN.

Program manager

meta@cesnet.cz

Homepage

URL: http://www.cpan.org/