eifunannot run

Run

Once you have configured your config files, you can run eifunannot on SLURM cluster like below:

$ sbatch -J eifunannot -o out_eifunnot.%N.%j.log -c 2 \\
  --mem 20G -p ei-long --wrap "source eifunannot-1.4.0 && \\
  /usr/bin/time -v eifunannot run --config run_config.yaml \\
  --ahrd_config ahrd_example_input_go_prediction.generic.yaml \\
  --hpc_config cluster_config.json --jobs 200"

Usage

$ eifunannot run --help
usage: eifunannot [-h] --config [CONFIG] --ahrd_config [AHRD_CONFIG]
                  [--hpc_config [HPC_CONFIG]] [--jobs [JOBS]] [-np]

EI FunAnnot version 1.4.0 - run

optional arguments:
  -h, --help            show this help message and exit
  --config [CONFIG]     Provide config.yaml file to run the pipeline (default: None)
  --ahrd_config [AHRD_CONFIG]
                        Provide ahrd_config.yaml file to run the pipeline (default: None)
  --hpc_config [HPC_CONFIG]
                        Provide hpc_config.json file (default: /ei/software/cb/eifunannot/1.4.0/x86_64/lib/python3.7/site-packages/eifunannot/config/cluster_config.json)
  --jobs [JOBS]         Maximum number of jobs to execute at any one time (default: 1)
  -np, --dry_run        Dry run (default: False)

Example run command:
eifunannot run --config [plants.yaml]

Contact:Gemy Kaithakottil (kaithakg)([email protected])