2. Example Usage¶

A workflow script is provided to allow users the ability to run locally or to submit to Biowulf SLURM.

2.1 Runmodes¶

There are several “flags” which have been created to run the commands. These are build, prepare, find, predict

bash metro_script.sh build echo

2.2 Handling Runmodes¶

There are several options for handing the above runmodes. These include:

1. echo: this will print the SH file location
2. cat: this will print the contents of the SH file
3. sh: this will run the SH file locally
4. submit_batch: this will run the SH file on the SLURM cluster (use HPC dashboard to monitor)
5. submit_batch_large: this will run the SH file on the SLURM cluster with “larger” resources

2.3 Examples to run the workflow:¶

Example printing out the workflow commands to the command line:

bash metro_script.sh build cat
bash metro_script.sh prepare cat
bash metro_script.sh find cat
bash metro_script.sh predict cat

Example submitting to SLURM:

bash metro_script.sh build submit_batch
bash metro_script.sh prepare submit_batch
bash metro_script.sh find submit_batch
bash metro_script.sh predict submit_batch_large