Perl - modules

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.

License

Differs according to used Perl module.

Availability

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of perl-modules and load default version of perl-modules as

module avail perl-modules/ # list available modules
module load perl-modules   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail perl-modules

and choose explicit version you want to use.

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 (2.132830), CPAN::Meta::Check (0.008), CPAN::Meta::Requirements (2.125), CPAN::Meta::YAML (0.010), Cache::Cache (1.06), 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::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 (5.28.1), 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), 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	Acme::Damn (0.08), Algorithm::Diff (1.1903), Algorithm::Diff::XS (0.04), Alien::Build (2.21), Alien::Libxml2 (0.16), App::Cmd (0.331), Archive::Any::Lite (), Array::Diff (), B::Hooks::OP::Check (0.22), Bio::SamTools (), Bit::Vector (7.4), Browser::Open (0.04), CPAN::DistnameInfo (), CPAN::Meta (2.150010), CPAN::Meta::Check (0.014), CPAN::Meta::Requirements (2.140), Cairo (1.106), Capture::Tiny (0.48), Carp::Clan (6.07), Chart::Plotly (0.014), Class::Accessor (), Class::Data::Inheritable (0.08), Class::Inspector (), Class::Load (0.25), Class::Load::XS (0.10), Class::Method::Modifiers (), Class::Tiny (), Class::XSAccessor (1.19), Clone (0.41), Compress::Raw::Bzip2 (2.101), Compress::Raw::Zlib (2.101), Const::Fast (0.014), DBD::Pg (3.10.0), DBD::SQLite (1.54), DBD::mysql (4.050), DBI (1.636), Data::Binary (), Data::Dump (1.23), Data::OptList (0.110), Data::Section (), Date::Parse (2.30), Devel::CheckLib (1.13), Devel::Cycle (), Devel::GlobalDestruction (), Devel::Hide (), Devel::OverloadInfo (0.005), Devel::StackTrace (2.04), Devel::Symdump (), Dist::CheckConflicts (0.11), Encode (3.01), Encode::Locale (1.05), Error (0.17027), Eval::Closure (0.14), Exception::Class (1.44), ExtUtils::Config (0.008), ExtUtils::Depends (0.8000), ExtUtils::Helpers (0.026), ExtUtils::InstallPaths (0.012), ExtUtils::MakeMaker::CPANfile (), ExtUtils::PkgConfig (1.16), FFI::CheckLib (0.26), File::BaseDir (), File::Copy::Recursive (), File::DesktopEntry (), File::Find::Object (), File::Listing (6.04), File::MimeInfo (), File::ReadBackwards (), File::ShareDir (), File::ShareDir::Install (), File::chdir (), File::pushd (1.016), GD (2.71), Getopt::Long::Descriptive (0.104), Graph (), HMMER2GO (), HTML-TableExtract (), HTML::Parser (3.72), HTML::Show (0.001), HTML::Tagset (3.20), HTTP::Cookies (6.04), HTTP::Daemon (6.01), HTTP::Date (6.02), HTTP::Message (6.18), HTTP::Negotiate (6.01), IO (1.39), IO::All (), IO::CaptureOutput (1.1104), IO::Compress (), IO::HTML (1.001), IO::Stringy (), IO::TieCombine (1.005), IO::Tty (1.12), IPC::Run (20180523.0), IPC::System::Simple (1.25), Importer (0.025), Inline (), Inline::C (), JSON (4.02), LWP::MediaTypes (6.02), Lingua::EN::Inflect (), List::MoreUtils (0.416), List::MoreUtils::XS (0.428), List::Util (1.50), MIME::Charset (), MRO::Compat (0.13), Mock::Config (0.03), Module::Build (0.4229), Module::Build::Tiny (0.039), Module::CPANfile (), Module::Find (), Module::Implementation (0.09), Module::Pluggable (5.2), Module::Runtime (0.016), Module::Runtime::Conflicts (0.003), Module::Signature (), Moo (), Moose (2.2012), MooseX::ExtraArgs (0.02), Net::HTTP (6.18), Package::DeprecationManager (0.17), Package::Stash (), Package::Stash::XS (0.29), PadWalker (2.3), Parallel::ForkManager (2.02), Params::Util (1.07), Params::Validate (1.29), Parse::RecDescent (), Path::Tiny (0.108), Pegex (), Perl (5.28.1), Perl::Unsafe::Signals (0.03), Pod::Coverage (), Pod::Spell (), Pod::Spell::CommonMistakes (), Ref::Util (0.204), Ref::Util::XS (0.117), Regexp::Common (2017060201), Regexp::Trie (), Role::Tiny (), SVG (), Scope::Guard (0.21), Set::Scalar (), Software::License (), Statistics::R (), String::RewritePrefix (0.008), Sub::Exporter (0.987), Sub::Exporter::Progressive (), Sub::Info (0.002), Sub::Install (0.928), Sub::Name (0.21), Sub::Quote (), Sub::Uplevel (0.2800), Sys::SigAction (), Term::ReadKey (2.37), Term::Size::Any (), Term::Size::Perl (), Term::Table (0.015), Test2::Suite (0.000127), Test::Base (), Test::CleanNamespaces (0.24), Test::Deep (1.128), Test::Differences (0.67), Test::Exception (0.43), Test::FailWarnings (), Test::Fatal (0.014), Test::File (), Test::Fork (), Test::LeakTrace (0.16), Test::Memory::Cycle (), Test::MockRandom (), Test::More::UTF8 (0.05), Test::Most (0.35), Test::Needs (0.002006), Test::Number::Delta (), Test::Pod (), Test::Pod::Coverage (), Test::Regexp (2017040101), Test::Requires (0.10), Test::RequiresInternet (), Test::Simple (1.302169), Test::UseAllModules (), Test::Warn (0.36), Test::Warnings (0.027), Test::Weaken (), Test::YAML (), Test::utf8 (), Text::CSV_XS (1.39), Text::Diff (1.45), Text::Format (), Text::NSP (1.31), Text::Template (1.58), Try::Tiny (0.30), UUID::Tiny (1.04), Unicode::LineBreak (2019.001), Unicode::UTF8 (0.62), WWW::RobotRules (6.02), Want (0.29), XML::DOM (), XML::DOM::XPath (), XML::Filter::BufferText (), XML::LibXML (2.0204), XML::NamespaceSupport (1.12), XML::Parser (2.44), XML::RegExp (), XML::SAX (1.00), XML::SAX::Base (1.09), XML::SAX::Writer (), XML::Simple (2.25), XML::Twig (), XML::Writer (), XML::XPathEngine (), XSLoader (0.24), YAML (1.27), YAML::LibYAML (0.80), bareword::filehandles (0.006), forks (0.36), indirect (0.38), install (0.01), libwww::perl (), libxml-perl (), multidimensional (0.014), strictures ()
bioperl-1.7.8-gcc	Algorithm::Diff (1.201), Alien::Build (2.51), Alien::Libxml2 (), Capture::Tiny (0.48), Class::Data::Inheritable (0.09), Data (), Date::Parse (2.33), Devel::Cycle (1.12), Devel::StackTrace (2.04), Encode::Locale (1.05), Error (0.17029), Exception::Class (1.45), Exporter::Tiny (1.002002), ExtUtils::Config (0.008), ExtUtils::Helpers (0.026), ExtUtils::Install (2.20), ExtUtils::InstallPaths (0.012), FFI::CheckLib (0.28), File::Listing (6.15), File::Remove (1.61), File::Which (1.27), File::chdir (0.1010), Getopt::Long (2.52), HTML::Tagset (3.20), HTTP::Cookies (6.10), HTTP::Daemon (6.14), HTTP::Date (6.05), HTTP::Message (6.37), HTTP::Negotiate (6.01), Heap (0.80), IO::HTML (1.004), IO::String (1.08), IO::Stringy (2.113), IPC::Run (20220807.0), Importer (0.026), LWP::MediaTypes (6.04), Module::Build (0.4231), Module::Build::Tiny (0.039), Module::Install (1.19), Module::Pluggable (5.2), Module::ScanDeps (1.31), Mojo::DOM58 (3.001), Net::HTTP (6.22), Number::Format (1.75), Path::Tiny (0.122), Perl (5.32.1), Regexp::Common (2017060201), Scope::Guard (0.21), Set::Scalar (1.29), Sort::Versions (1.62), Spiffy (0.46), Statistics::Basic (1.6611), Statistics::R (0.34), Sub::Info (0.002), Sub::Uplevel (0.2800), Switch (2.17), Term::Table (0.016), Test2::Suite (0.000145), Test::Base (0.89), Test::Deep (1.130), Test::Differences (0.69), Test::Exception (0.43), Test::Fatal (0.016), Test::Most (0.37), Test::Needs (0.002009), Test::Requires (0.11), Test::RequiresInternet (0.05), Test::Simple (1.302191), Test::Warn (0.36), Test::Weaken (3.022000), Test::YAML (1.07), Text::Diff (1.45), Try::Tiny (0.31), URI (5.12), WWW::RobotRules (6.02), XML::Filter::BufferText (1.01), XML::NamespaceSupport (1.12), XML::RegExp (0.04), XML::SAX (1.02), XML::SAX::Base (1.09), XML::SAX::Writer (0.57), XML::Writer (0.900), YAML (1.30), YAML::Tiny (1.73)

Use

Initialize environment with command:

module add bioperl-1.7.8-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-1.7.8-gcc
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.

Documentation

Perl modules documentation is available through CPAN.

Homepage

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