The BioLockJ program is launched through the biolockj script. See biolockj --help.

Support programs can access information about BioLockJ modules and properties through biolockj-api.

There are also several helper scripts for small specific tasks, these are all found under $BLJ/script and added to the $PATH after the basic installation:

Bash Commands#

Command	Description
last-pipeline	Get the path to the most recent pipeline. ideal for: cd $(last-pipeline) ls `last-pipeline`
cd-blj	Go to most recent pipeline & list contents. This is not a script, it is an alias that is added to your bash profile by the install script. The line defining it should look like: alias cd-blj='cd $(last-pipeline); quick_pipeline_view'
quick_pipeline_view	essentially just pwd and ls; designed for the cd-blj alias.
blj_reset	Reset pipeline status to incomplete. If restarted, execution will start with the current module.

Deprecated Commands#

Command	Description (Replacement)
blj_log	Tail last 1K lines from current or most recent pipeline log file. Replacement: cd $(last-pipeline); tail -1000 *.log
blj_summary	Print current or most recent pipeline summary. Replacement: cd $(last-pipeline); cat summary.txt
blj_complete	Manually completes the current module and pipeline status. This functionality should never be needed. For the rare occasions when it is appropriate, it can be done manually. Replacement: touch biolockjComplete
blj_reset	Reset pipeline status to incomplete. If restarted, execution will start with the current module. The need for this functionality is common; and a bash wrapper script still exists. Alternative: java -cp ${BLJ}/dist/BioLockJ.jar biolockj.launch.Reset ${PWD}
blj_download	If on cluster, extract and print the command syntax from the summary.txt file to download pipeline results to your local workstation directory: pipeline.downloadDir. no replacement: You will need to review your pipelines summary file to find the download command.