interproscan_docker

Container recipes for building Interproscan (for Docker and Singularity).

• If you want to use Interproscan external privative software, these programs must be obtained first with granted academic permissions.
  • SignalP signalp-4.1b.Linux.tar.Z
  • TMHMM tmhmm-2.0c.Linux.tar.gz
  • Phobious phobius101_linux.tar.gz
    • Regarding phobius: https://www.biostars.org/p/238642/
  • Keep in mind that some other modifications are also needed in those programs above in advance, e. g., replacing /usr/bin/perl for /usr/bin/env perl

Last software package versions of Interproscan include the whole data by default. For container performance and distribution, we don't keep Interproscan data directory.

Pregenerated images

• Singularity
• Docker

Building from Docker recipes

# With privative software
docker build -t iprscan:5.72-103.0 -f Dockerfile .
sudo singularity build iprscan-5.72-103.0.sif docker-daemon://iprscan:5.72-103.0
# Without privative software
docker build -t iprscan-open:5.72-103.0 -f Dockerfile.open .
sudo singularity build iprscan-5.72-103.0.open.sif docker-daemon://iprscan-open:5.72-103.0

You can avoid using sudo with --fakeroot Singularity build option.

Running

For running the container images, it is mandatory to mount a data directory that fits the same Interproscan version. Below some example commands:

# Docker
docker run --volume /path/to/data:/usr/local/interproscan/data --volume /path/to/scratch:/scratch -t biocorecrg/interproscan:5.72-103.0 /usr/local/interproscan/interproscan.sh -i /scratch/test.fa --goterms --iprlookup --pathways -o /scratch/out_interpro -f TSV

# Singularity
singularity exec -B /path/to/data:/usr/local/interproscan/data -e iprscan-5.72-103.0.open.sif /usr/local/interproscan/interproscan.sh -i /path/to/test2.fa --goterms --iprlookup --pathways -o /path/to/out_interpro -f TSV

NOTES

• Moreover, keep into account that a user with suitable permissions may need first to index /usr/local/interproscan/data directory (e.g., with python3 /usr/local/interproscan/initial_setup.py). You can use the very container images. Details here: https://interproscan-docs.readthedocs.io/en/latest/HowToRun.html
• Depending on your setup, you may need to change SINGULARITY_TMPDIR (and SINGULARITY_CACHEDIR) environment variables for pointing to a location with enough space. More details at: https://singularity.hpcng.org/admin-docs/master/installation.html