- Description
- InterProScan runs the scanning algorithms from the InterPro database in an integrated way.
- Modulefile
interproscan- Documentation
- InterPro homepage
- Notes
- The precalculated match lookup service is not available from the compute nodes, and should be disabled with the
-dp flag. See examples below.
- We do not support running InterProScan spanning multiple hosts (CLUSTER mode), but you can still run InterProScan on a single node with multiple CPU cores.
- Always submit your jobs with the request for 4 CPU cores, like so: "
-pe openmp 4". The reason for this requirement is the fact that the software is centrally installed and users have no write access to the file interproscan.properties, which sets the number of workers and threads as 2 by 2. According to our tests, Java's own overhead is minimal, and thus four CPU slots are adequate.
- Usage
- Here is an example of a submission script:
#$ -cwd
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G
#$ -pe openmp 4
module purge
module load gcc openmpi/gcc python/2.7.2 java interproscan
interproscan.sh -i $INTERPROSCAN/test_proteins.fasta -f tsv -dp
- Here is another example using a Local Scratch directory for temporary files:
#$ -cwd
#$ -l h_rt=1:0:0
#$ -l h_vmem=4G
#$ -pe openmp 4
module purge
module load gcc openmpi/gcc python/2.7.2 java interproscan
interproscan.sh -i 83333.fasta -dp -f tsv,html --goterms -T $TMPDIR