Commands

BioLockJ commands are located under $BLJ/script

Command	Description
biolockj [config_path]	Start a pipeline using the Configuration properties in [config_path]. Pipeline output directory is created under $BLJ_PROJ.
blj_build	Run build.xml ant script to build BioLockJ.jar from Java source code.
blj_complete	Manually completes the current module and pipeline status.
blj_config	The install script updates ~/.bash_profile to call blj_config. Adds BioLockJ Commands into your $PATH & sets program variables: $BLJ: BioLockJ application directory. $BLJ_SCRIPT: BioLockJ script directory containing executable script files. $BLJ_PROJ: Root pipeline directory used in multiple Commands.
blj_downlaod	If on cluster, print command syntax to download current or most recent $BLJ_PROJ pipeline analysis to your local workstation directory: pipeline.downloadDir.
blj_functions	This script contains common functions used in BioLockJ.
blj_go	Go to most recent $BLJ_PROJ pipeline & list contents.
blj_log	Tail last 1K lines from current or most recent $BLJ_PROJ pipeline log file.
blj_reset	Reset pipeline status to incomplete. If restarted, execution will start with the current module.
blj_summary	Print current or most recent $BLJ_PROJ pipeline summary.