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.

It is important to ensure that program and data versions match and that this is adequately reflected in interproscan.properties or interproscan.open.properties files. Otherwise Interproscan is not likely to work.

Pregenerated images

• Singularity
• Docker

Building from Docker recipes

# With privative software
docker build -t iprscan:5.56-89.0 -f Dockerfile .
sudo singularity build iprscan-5.56-89.0.sif docker-daemon://iprscan:5.56-89.0
# Without privative software
docker build -t iprscan-open:5.56-89.0 -f Dockerfile.open .
sudo singularity build iprscan-5.56-89.0.open.sif docker-daemon://iprscan-open:5.56-89.0

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:5.56-89.0 /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-5.56-89.0.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