Managing Perl libraries across nodes

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Revision as of 11:50, 4 October 2007 by Tharris (talk | contribs)
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Standardizing modules across nodes

To standardize modules across nodes (and avoid the headache of having to update each node separately with new libraries), I am now including required perl modules with the WormBase software. This includes modules for both different versions of Perl and different architectures.

NOTE: Although this general approach works, dynamically modifying @INC (in say perl.startup) to include an architecture specific but private path doesn't work. Perl won't automatically cascade through child directories.

In addition, packlist is still installed in system paths, even when installing using PREFIX and LIB. This means that there can be a disconnect of what Perl things is currently installed if moving from private to public install libraries. e.g.

cpan> CGI cpan> CGI already up-to-date

(even though the system copy may not be)

Configuring the primary build environment

Brie3 acts as the primary staging environment. At the end of this configuration, we will be left with a new directory at /usr/local/wormbase/extlib containing all necessray Perl modules for a WormBase installation. This directory is automatically mirrored into the staging directory (/usr/local/wormbase-production), and from there distributed to production nodes as necessary.

The intial configuration of the system followed these steps:

Configure CPAN

The first time you launch CPAN, you will be prompted to configure it. Specially, we need to configure CPAN to install modules in our special WormBase directory.

$ perl -MCPAN -e shell (note: we do NOT need to be a privileged user) cpan> o conf init (only necessary if not prompted)

For the Makefile.PL arguments, enter

 PREFIX=/usr/local/wormbase/extlib \ 
 LIB=/usr/local/wormbase/extlib/lib \

TH - Note to self: It might be cleaner to just flatten this whole structure into a single directory using something like...

PREFIX=/usr/local/wormbase/extlib \


PREFIX=/usr/local/wormbase/extlib \
VENDORPREFIX=/usr/local/wormbase/extlib \

Initial module list

Some of the following commands may be redundant depending on module dependencies

Note: Some of these modules may be architecture-dependent. For the most part, most of the WormBase servers are i686. If you encounter problems with the included modules and you are working on a non i686 system, try installing these modules first. The site-specific module paths for your Perl will be searched first.

cpan> install Bundle::CPAN
cpan> install IO::Compress::Gzip 
cpan> install LWP
cpan> install CGI
cpan> install CGI::Session
cpan> install CGI::Cache
cpan> install Cache::Cache
cpan> install Cache::Filecache
cpan> install SVG
cpan> install GD       <------ architecture dependent!
cpan> install GD::SVG
cpan> install Digest::MD5
cpan> install HTML::Parser
cpan> install HTML::TokeParser
cpan> install IO::Scalar
cpan> install IO::String
cpan> install Net::FTP
cpan> install SOAP::Lite
cpan> install Statistics::OLS
cpan> install Storable
cpan> install Text::Shellwords
cpan> install WeakRef
cpan> install MIME::Parser
cpan> install XML::SAX
cpan> install XML::Parser::Lite
cpan> install SVG::Graph
cpan> intsall XML::Writer
cpan> install XML::Twig
cpan> install Test::Pod
cpan>install DBI
cpan>install DBD::mysql

Install AcePerl

This can probably be done through CPAN but I prefer to install from source.

perl Makefile.PL `cat /usr/local/wormbase/conf/Makefile.params`

Build BioPerl

Install / update BioPerl:

cd /usr/local/wormbase-lib/bioperl-production perl Build.PL --install_base /usr/local/wormbase/extlib --install_path lib=/usr/local/wormbase/extlib ./Build ./Build install // Note: you DO NOT NEED root privileges.

Build GBrowse

Rebuild Gbrowse placing libraries into our extlib/.

perl Makefile.PL LIB=/usr/local/wormbase/extlib/lib/perl5/site_perl/5.8.8 \
   CONF=/usr/local/wormbase/conf \
   HTDOCS=/usr/local/wormbase/html \
   CGIBIN=/usr/local/wormbase/cgi-perl/seq \
make install

Adjust @INC

@INC needs to be adjusted so that wormbase can find the local copies of modules. We want to append the extlib path to our @INC using perl.startup. This allows us to easily override architecture-dependent modules on any of the nodes as necessary.

Preparing Nodes

To prepare individual production nodes:

It shouldn't be necessary to adjust your @INC, but it might be useful. You might also want to append


to your path.

Synchronizing libraries

Library syncrhonization is handled by two scripts.

1. Copy /usr/local/wormbase/extlib to /usr/local/wormbase-production/extlib

This step is not automated to avoid accidentally pushing libraries to production nodes. Remember, wormbase-production is the rsync target for all of the nodes.

2. New libraries will automatically be synced onto the production nodes during the next update. If you want to push software/libraries onto the nodes before then, see [[Updating_software_on_production_nodes Updating software on production nodes].