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= local::lib = | = local::lib = |
Revision as of 16:36, 7 January 2011
Contents
Overview
Maintaining Perl modules across our server farm can be a time consuming and tedious task because of the heterogeneity of our setup. Further, we often need to maintain unique sets of libraries for different applications with collisions.
To solve these problems, I maintain local copies of libraries for each application. Typically, these are found at
/path/to/application/extlib
Installing modules in a local path is made significantly easier through the use of local::lib and Apache2/mod_perl2 "PerlSwitches" directive.
local::lib dispenses with the need to maintain multiple CPAN configurations or manual tweaks to your environment variables in order to recognize already installed modules.
Installing a local CPAN repository
I maintain a local mirror of CPAN. This makes installing our web application significantly faster.
$ sudo perl -MCPAN -e shell $ cpan> install CPAN::Mini
Create a minicpanrc file at ~/
# CPAN::Mini configuration file # to set up our local WormBase CPAN local: /usr/local/wormbase/minicpan remote: http://mirror.rit.edu/CPAN/ exact_mirror: 1
Set up your CPAN to use the local mirror:
$ cpan cpan> o conf set urllist file:///usr/local/wormbase/minicpan/ cpan> o conf commit
Set up the minicpan to run once a day:
- 3 * * * minicpan
Private library locations
By convention, 3rd party Perl modules are maintained in an "extlib" directory within each project directory:
website-classic/extlib - The "Classic" WormBase website website/extlib - 'The rearchitecture website-2.01/extlib - Version 2.01 of the rearchitecture
And so on...
Required Perl modules
WormBase "Classic"
Install the following Perl modules via CPAN. Note that you DO NOT AND SHOULD NOT be sudo.
cd /usr/local/wormbase/extlib/classic perl -Mlocal::lib=./ eval $(perl -Mlocal::lib=--self-contained,./) perl -MCPAN -e 'CPAN::install(MODULE)'
// Some basics... YAML LWP ExtUtils::MakeMaker Bundle::CPAN // The rest... Bio::Graphics BioPerl // When prompted, choose to download all optional modules. This will also install Ace: Ace // During configuration, choose option (3), then set the remaining variables as follows: Site-specific configuration files: /usr/local/wormbase/website-classic/conf CGI path: /usr/local/wormbase/website-classic/cgi-bin HTML path: /usr/local/wormbase/website-classic/html
// For Catalyst-based apps: Site-specific configuration files: /usr/local/wormbase/website/conf CGI path: /usr/local/wormbase/website/root/cgi HTML path: /usr/local/wormbase/website/root/static
Cache::Cache Cache::FileCache CGI CGI::Session CGI::Cache CGI::Toggle Class::Base Data::Stag Date::Calc Date::Manip DB_File DBI DBD::mysql (mysql devel package must be installed first) // To build by hand: perl Makefile.PL INSTALL_BASE=/usr/local/wormbase/extlib/classic --testuser=USER --testpassword=PASS make ; make test ; make install Digest::MD5 Flickr::API Flickr::API::Simple // This is a private library cd /usr/local/wormbase/build perl ./Build.PL --install_base /usr/local/wormbase/extlib/classic ./Build install GD GD::SVG GD::Graph GD::Graph::pie HTML::TokeParser IO::Scalar IO::String Image::GD::Thumbnail Log::Log4perl MIME::Lite mod_perl2 // Requires that apache2 already be installed; apxs is at /usr/local/apache2/bin/apxs Net::FTP Proc::Simple Search::Indexer SOAP::Lite Statistics::OLS Storable SVG SVG::Graph Term::ReadKey Test::Pod Text::Shellwords Time::Format WeakRef XML::SAX XML::Parser XML::DOM XML::Writer XML::Twig XML::Simple
local::lib
Installation
local::lib is installed into the system Perl path:
sudo perl -MCPAN -e install 'local::lib'
Setting a library path
$ cd /usr/local/wormbase/extlib/classic $ perl -Mlocal::lib=./ export MODULEBUILDRC="/usr/local/wormbase/extlib/classic/.modulebuildrc" export PERL_MM_OPT="INSTALL_BASE=/usr/local/wormbase/extlib/classic" export PERL5LIB="/usr/local/wormbase/extlib/classic/lib/perl5:/usr/local/wormbase/extlib/classic/lib/perl5/x86_64-linux-gnu-thread-multi:$PERL5LIB" export PATH="/usr/local/wormbase/extlib/classic/bin:$PATH"
Take note: we will use some of these variables for, say, setting up apache.
$ eval $(perl -Mlocal::lib=--self-contained,./)
Installing a module
$ perl -MCPAN -Mlocal::lib=--self-contained -e 'CPAN::install(MODULE)'
Installing a module without using local::lib
You may on occasion need to install something without using local::lib. For EUMM modules, use
perl -I/usr/local/wormbase/[PROJECT]/extlib Makefile.PL INSTALL_BASE=/usr/local/wormbase/[PROECT]/extlib
And for Module::Build
perl -I/usr/local/wormbase/[PROJECT]/extlib Makefile.PL --install_base /usr/local/wormbase/[PROJECT]/extlib
Alternatively, you can manually edit ~/.cpan/CPAN/MyConfig.pm
Tips and Tricks
Some modules may require a little TLC. After running the script you can find source at ~/.cpan/build/module-*
BioPerl
Instead of building BioPerl from CPAN, it might be necessary to build from SVN:
$ cd /usr/local/wormbase/build $ svn co svn+ssh://USERNAME@dev.open-bio.org/home/svn-repositories/bioperl/bioperl-live/trunk bioperl-live $ mv bioperl-live bioperl-live-tharris $ cd bioperl-live-tharris $ perl ./Build.PL install_base /usr/local/wormbase/extlib $ ./Build test $ ./Build install
DBD::mysql
You will need to specify a test user and test password for tests to pass.
ModPerl2
You will need to be sudo in order to install the dso.
Updating Modules
To show all modules that are out-of-date with those on CPAN:
$ cd /path/to/extlib $ perl -Mlocal::lib=./ $ eval $(perl -Mlocal::lib=--self-contained,./) $ perl -MCPAN -e 'CPAN::Shell->r'
To update all of these modules at once:
$ perl -MCPAN -e 'CPAN::Shell->install(CPAN::Shell->r)'
Managing libraries across architectures
Via CPAN bundles
# Create a bundle $ cd /path/to/extlib $ perl -Mlocal::lib=./ $ eval $(perl -Mlocal::lib=--self-contained,./) $ perl -MCPAN -e autobundle # The bundle is (typically) in extlib
# To reinstall: $ perl -MCPAN -e 'install Bundle::Snapshot_YYYY_MM_DD_00'
(Or just use the install script).