How to Use InterProScan via Container

InterProScan can be used via Docker or Singularity to simplify the installation and execution process in different computing environments.

Before using InterProScan 5 via container, make sure you are using Linux operating system and you have Docker or Singularity installed and running on your system.

The image (https://hub.docker.com/r/interpro/interproscan) does not include the data required to run InterProScan, which needs to be downloaded separately.

Get InterProScan data

For the latest InterProScan release (5.68-100.0), data can be downloaded with the following command:

curl -O http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.68-100.0/alt/interproscan-data-5.68-100.0.tar.gz

We always recommend verifying your downloads for corruption:

curl -O http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.68-100.0/alt/interproscan-data-5.68-100.0.tar.gz.md5
md5sum -c interproscan-data-5.68-100.0.tar.gz.md5

Finally, extract data files from the downloaded archive:

tar -pxzf interproscan-data-5.68-100.0.tar.gz

The data will be extracted to interproscan-5.68-100.0/data.

Using Docker

Pull the image:

docker pull interpro/interproscan

Example:

Create the directories for temporary and output files, respectively:

mkdir temp output

Run the image:

docker run --rm \
-v $PWD/interproscan-5.68-100.0/data:/opt/interproscan/data \
-v $PWD/output:/output \
-v $PWD/temp:/temp \
interpro/interproscan:5.68-100.0 \
--input /path/to/your/file.fasta \
--disable-precalc \
--output-dir /output \
--tempdir /temp \
--cpu 16

Using Singularity

Pull the image:

singularity pull docker://interpro/interproscan:latest

Example:

Create the directories for temporary and output files, respectively:

mkdir temp output

Run the image:

singularity exec
    -B $PWD/interproscan-latest/data:/opt/interproscan/data \
    -B $PWD/output:/output \
    -B $PWD/temp:/temp \
    -B $PWD:/input \
    interproscan_latest.sif \
    /opt/interproscan/interproscan.sh \
    --input /input/your.fasta \ \
    --disable-precalc \
    --output-dir /output \
    --tempdir /temp \
    --cpu 16 \

NOTE: In Singularity, it is necessary to provide the full path to the interproscan.sh script.