First of all, you will have to edit scripts to meet YOUR requirements:
- edit "blast_template.txt": this is the script that is scheduled by PBS on the computing system. Among others, it contains queries and subjet banks to use, as well as BLAST and PLAST commands to run.
- edit "01-generate-scripts.sh": this is the script that defines PBS constraints (number of cores, memory and walltime).
Then, simply execute scripts by sequential order:
- first, run 01-generate-scripts.sh: takes "blast_template.txt" and generate as many job submission scripts as PBS constraints (cores and comparison types)
- then, run[ 02-submit-scripts.sh](scripts/ 02-submit-scripts.sh): automatically submits to PBS all the scripts generated by previous step
- optionally, run 03-alter-wtime.sh: alters walltime of all submitted jobs (in case your jobs take a long time to finish)
- finally, run 04-analyse-resources.sh: compiles usefull data from jobs stats; for instance, this is the script used to generate content of sub-folder results
Scripts with "HTC" in their name are intended to be used with HTC-BLAST 4.3 framework.