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.
For the latest InterProScan release (5.67-99.0), data can be downloaded with the following command:
curl -O http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.67-99.0/alt/interproscan-data-5.67-99.0.tar.gz
We always recommend verifying your downloads for corruption:
curl -O http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.67-99.0/alt/interproscan-data-5.67-99.0.tar.gz.md5
md5sum -c interproscan-data-5.67-99.0.tar.gz.md5
Finally, extract data files from the downloaded archive:
tar -pxzf interproscan-data-5.67-99.0.tar.gz
The data will be extracted to interproscan-5.67-99.0/data.
Pull the image: :: docker pull interpro/interproscan
Create the directories for temporary and output files, respectively:
mkdir temp output
Run the image:
docker run --rm \
-v $PWD/interproscan-5.67-99.0/data:/opt/interproscan/data \
-v $PWD/output:/output \
-v $PWD/temp:/temp \
interpro/interproscan:5.67-99.0 \
--input /path/to/your/file.fasta \
--disable-precalc \
--output-dir /output \
--tempdir /temp \
--cpu 16
Pull the image: :
singularity pull docker://interpro/interproscan:latest
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.