Usage

To run ARC copy the $HPC_ARC_CONF/ARC_config.txt file to your current working directory and adjust it for your analysis.

cp $HPC_ARC_CONF/ARC_config.txt /path/to/your/desired/directory

In preparing your ARC_config.txt file, be careful in how things are named. Do not start a non-numerical parameter with a number. ARC checks if the parameter starts with a number, and if it does, assumes the whole parameter is a number and tries to convert to integer.

For example a reference file that is named 5_genes.fasta would throw an error because ARC sees the 5, assumes the parameter is a number and tries to convert "5_genes.fasta" into an integer.