AUTO DEPLOY
===========
This repo is automatically deployed after push to origin/master via Jenkins job 'Deploy wugc-hudson.'

SYMLINKS
========
current/pipeline        The default snapshot for the cron/pipeline. (Must pass the test suite, build tests and build diffs.)
current/user            The in the new PERL5LIB and PATH for users. (Must pass the test suite.)
current/web             The default snapshot for the web interface.

SUB-DIRECTORIES
===============
annotation/bin          Annotation cron scripts.
snapshots/custom        Snapshots which have been custom built, e.g. hotfixes or one-offs.
snapshots/old           Snapshots which have been superseded and have no running builds.
snapshots               Snapshots which have passed all tests go into this base directory.

SNAPSHOT "ANATOMY"
==================
source_dirs.txt         Contains the locations of each git repo from which the snapshot was made.
revisions.txt           Contains the commit hash for the HEAD of each git repo from which the snapshot was made.
previous_version.txt    Contains the 'genome-N' tag of the version from which the snapshot was promoted.
git-changelog           Contains the 'git log' of the previous version to the current; generated with bin/changelog.
CHANGE_SUMMARY          Contains the email body for announcement messages.

All other files come from the git repos.

CONFIGURATION
=============
lib/Defaults.pm         Contains several variables to customize and configure your Genome Hudson configuration.

COMMANDS
========
bin/annotation-sync-ncbi-db Syncs the annotation nt/nr databases
bin/apipe_tests             Runs the builds, executed by run_builds.
bin/changelog               Generates the git changelog.
bin/diff_builds             Runs the build diff tests.
bin/email_failures          Parses the JUnit XML and determines who should be contacted (via git) as to who should be contacted.
bin/genome-sync             Wrapper for the syncrhonize command modules under Site/TGI/Synchronize.
bin/hotfix                  Automatic creation of fix snapshosts given some git repos and commits.
bin/init                    Initialize Genome Hudson.
bin/promote                 Promote snapshot by symlinking into current.
bin/run_builds              Runs the build tests.
bin/run_tests               Runs the test suite.
bin/snapshot_status         Checks if a snapshot is still be used and optionally move it to old if not.