The pipeline contains wrappers to run tools in each assembly steps. Each script is written and tested to run on a slurm scheduler.

To begin, add the path to the pipeline in ~/.bash_profile :

export VGP_PIPELINE=/path/to/git/vgp-assembly/pipeline
export tools=/path/to/tools/installed

Try ./_submit_ in your desired step to see required input files. Most of the scripts only require a .fasta file as input.

The _submit are wrappers to submit jobs to launch the actual scripts.

Tools are loaded as modules. Adjust the module load part to your own environment.