InterProScan-Docker

A Dockerfile and associated tools for deploying containerized InterProScan5.

The Dockerfile is based-off the one used by EBI Metagenomics team but it has been modified to enable all InterProScan5 analyses with the exception of SignalP, Phobius, Tmhmm. These are excluded as they require licence agreements.

Building:

docker build https://raw.githubusercontent.com/Micromeda/InterProScan-Docker/master/Dockerfile -t micromeda/interproscan-docker

Usage:

Standard usage would be to use docker's -v flag to mount host analysis directories and pass the required interproscan.sh flags into the container.

Usage: docker run --rm --name interproscan -v /tmp:/tmp micromeda/interproscan-docker -dp --goterms --pathways -f tsv \
                  --appl "PfamA,TIGRFAM,PRINTS,PrositePatterns,Gene3d" -o /tmp/out.ipr -i /tmp/test.fasta

Inside the container interproscan.sh is called making the above equivalent to:

interproscan.sh -dp --goterms --pathways -f tsv --appl "PfamA,TIGRFAM,PRINTS,PrositePatterns,Gene3d" -o /tmp/out.ipr \
                -i /tmp/test.fasta

For convenience we have added run_docker_interproscan.sh that wraps the above commands. By default, this script will automatically set the number of number of workers and threads per job.

run_docker_interproscan.sh fasta.faa

You can also to manually specify the number of workers and threads per job.

# run_docker_interproscan.sh <FASTA> [NUMBER OF WORKERS] [NUMBER OF THREADS PER JOB]
run_docker_interproscan.sh fasta.faa 8 2