Installing the Web Application

From WormBaseWiki

Contents 1 NOTES 2 Install Catalyst 3 Check out the code 3.1 Create a directory for the Web Application 3.2 Fetch the code from the subversion repository 4 Install third party libraries 4.1 Install BioPerl 4.2 Install GBrowse 4.3 Install Ace 5 Additional Requirements

NOTES

1. Here, $ROOT refers to the root path to the web application. This can be located anywhere on the filesystem that you choose. If installing in a system path, you'll need to have sufficient privileges -- and adjust privileges of files as noted below.

2. You will need to have MySQL and AceDB installed locally. If you do not, edit $ROOT/wormbase.yaml as appropriate.

Install Catalyst

WormBase uses the Catalyst MVC Web Framework. Documentation on how to install it can be found in the Catalyst Manual.

To install it and all of its core modules in system paths:

   $ perl -MCPAN -e 'install Task::Catalyst'
   $ perl -MCPAN -e 'install Catalyst::Devel'

If your CPAN is set to prompt for dependencies, be prepared to press return often.

Install some additional requirements.

  $ perl -MCPAN -e 'install Catalyst::Model::DBI'
  $ perl -MCPAN -e 'install Catalyst::Model::Adaptor'
  $ perl -MCPAN -e 'install Catalyst::Plugin::Session'
  $ perl -MCPAN -e 'install Catalyst::Plugin::Session::State'
  $ perl -MCPAN -e 'install Catalyst::Plugin::Session::State::Cookie'
  $ perl -MCPAN -e 'install Catalyst::Plugin::Session::Store::FastMMap'
  $ perl -MCPAN -e 'install Catalyst::Action::RenderView'
  $ perl -MCPAN -e 'install Catalyst::Action::Rest'
  $ perl -MCPAN -e 'install Catalyst::Log::Log4Perl'
  $ perl -MCPAN -e 'install Test::YAML::Valid'

Check out the code

Create a directory for the Web Application

mkdir $ROOT  // ie ~/projects/wormbase

// For non-private paths only
sudo chgrp wormbase $ROOT
sudo chmod 2775 $ROOT

Fetch the code from the subversion repository

cd $ROOT

Then:

svn checkout svn+ssh://brie3.cshl.org/usr/local/svn/website

This command will check out the website code, including the trunk, tags, and branches directories. Look in "trunk" for the current version of the code.

Install third party libraries

The sources of select third party libraries are maintained along side the web application. This makes distribution and updates easier than installing items in system paths.

Install BioPerl

cd $ROOT
./install/bioperl.sh

When prompted for "Install optional modules...", choose [n], none. You'll need to install desired modules manually.

When prompted for "Install [a]ll Bioperl scripts, [n]one, or choose groups [i]nteractively", choose none.

Install GBrowse

cd $ROOT
./install/gbrowse.sh

NOTE: This fails on MacOSX. INSTALLSITESCRIPT in the Makefile.PL needs to be set $OPTIONS{BIN}.

Install Ace

 sudo perl -MCPAN -e shell
 cpan> install Ace

 What do you want to build?

  1) Interface to Ace socket server and local databases (pure Perl)
  2) The above plus XS optimizations (requires C compiler)
  3) The above plus RPC server interface (requires C compiler)

 Enter your choice:  [1] 

 Do you want to install Ace::Browser?  [n]

Additional Requirements

• Catalyst::Plugin::ConfigLoader
• Test::YAML::Valid