Collection of script templates

loop_over_job_submissions

Intent:

loop over list with input files for whom to perform same analysis per chromosome

Executable:

while_loop.sh

Input:

1. tmp.files.txt > text file with absolute file paths; one file per line
2. example_script.sh > analysis script which will be executed once per sample and chromosome

Usage:

./while_loop.sh

Possible Modifications:

• update files to work on by replacing tmp.files.txt
• update chromosome to work on by modifying array called chromosomes in while_loop.sh
• change analysis script by replacing example_script.sh

cluster_usage

Intent:

Based on UCL CS cluster, instead of using a loop to submit same job for numerous input files, setup a job array. Advantage is that the number of jobs to be run in parallel can be defined, which is of interest for especially demanding computations.

Executable:

test_array_scratch.sh

Input

-- none -- script created temporary test files

Usage

./test_array_scratch.sh