Perl package installation and manement

Tools

Package notes

CPAN is a great place to avoid reinvent the wheel, but some packages are not that reliable or not easy to use or install.

  • DBD::mysql. Follow this instruction. If you get something like “Library not loaded: libmysqlclient.16.dylib“, see here.
  • Interface to GNU Scientific Library Math::GSL. If you get lost at what the parameters are, read more in GSL manual, e.g. hypergeometric distribution.
  • Getopt::Long and Pod::Usage make a friendly command with options and help/man doc.
  • LSF (unauthorized!) – A perl API built on top of the LSF command line tools. I write my own version.
  • local::lib – create and use a local lib/ for perl modules with PERL5LIB (PS: best way to install package when you are not administrator.)
  • Dist::Zilla
  • FIle::Basename – Parse file paths into directory, filename and suffix.
  • Template Toolkit (TT) – website, book, and how to migarte from CGI
  • HTML::Table – set additional attribute by $table->setAttr("id=\"cluster_row\"");
  • Tree manipulation: Bio::TreeIO, Bio::Tree:Tree, Bio::Tree:TreeI, Bio::Tree::TreeFunctionsI, Bio::Tree::Node, Bio::Tree::NodeI
  • Perldoc server/mini CPAN: Pod::Webserver, Pod::POM::Web, Pod::Browser(Catalyst based), or CPAN::Mini::Webserver
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