Getting Started - RCChan5/BioLockJ GitHub Wiki
1. Complete Program Installation
- See Installation
2. Configure Program Input
- See Configuration
3. Start Your 1st Pipeline
-
To start your pipeline, pass your Configuration file path $CONFIG_PATH to the biolockj command:
> biolockj $CONFIG_PATH ============================================================ BioLockJ JAR: /projects/afodor_research/apps/BioLockJ/dist/BioLockJ.jar BioLockJ Config File: /projects/afodor_research/apps/BioLockJ/resources/test/config/hpc/testKraken.properties BioLockJ started successfully! ============================================================ -
Verify biolockj command output is accurate:
- BioLockJ JAR file path is valid
- BioLockJ Configuration file path is valid
- Verify message "BioLockJ started successfully!" is printed.
4. Check Pipeline Status
-
Check pipeline progress by tailing the pipeline Java log file with blj_go and blj_log:
> blj_go # Go to your newest pipeline > blj_log # Tail pipeline log file -
Verify java is running:
> ps -u $USER psu PID TTY TIME CMD 16499 pts/45 00:36:21 java 188510 pts/45 00:00:00 bash ... -
If running modules on the cluster, check status of BioLockJ scripts on the job queue (command depends on job queue implementation):
> qstat -u $USER Req'd Req'd Elap Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time ----------------------- ----------- -------- ---------------- ------ ----- ------ --------- --------- - --------- 530799.cph-m1.uncc.edu msioda cph_shor 04.0_PearMergeRe 44312 1 8 64gb 01:00:00 C 00:19:23 530800.cph-m1.uncc.edu msioda cph_shor 04.1_PearMergeRe 36453 1 8 64gb 01:00:00 R 00:05:23
5. Investigate Failed Pipelines
- Failed pipelines can be restarted to save the progress made by successful modules.
- See Failure Recovery for more information.
- Failure Recovery should be avoided until you have successfully completed your 1st pipeline.