Package: Interproscan

About: Protein sequence analysis & classification.

Version: 5.32

Added: 2016-03-25

Updated: 2019-01-09

Installation directory: /bioinfo/bin

Source directory: /bioinfo/installs/interproscan-5.32-71.0

Link: InterProScan

interproscan

Interproscan configuration

Interproscan uses a configuration file to set the number of CPUs for a job. The default system configuration file is at /bioinfo/installs/interproscan-5.32-71.0/interproscan.properties and is set to use 8 CPUs. Therefore, a default interproscan condor job should request 8 CPUs (and 8G of RAM).

To control the number of CPUs used by your job you can create your own configuration file:

cd ~
mkdir .interproscan-5
cp /bioinfo/installs/interproscan-5.32-71.0/interproscan.properties .interproscan-5/

Edit the configuration file with your preferred text editor and change one or both of the following settings:

worker.number.of.embedded.workers=1
worker.maxnumber.of.embedded.workers=7

In the above example 1 + 7 = 8 CPUs will be used. See the interproscan documentation for more details. Generally increasing the worker.maxnumber.of.embedded.workers should be sufficient to increase the number of sequences analyzed in parallel.

Example interproscan HTCondor job file

universe                 = vanilla
getenv                   = true

request_cpus             = 8
request_memory           = 8G

notification             = Complete

ID                       = $(Cluster).$(Process)
output                   = interpro.$(ID).out
error                    = interpro.$(ID).err
log                      = interpro.$(ID).log
###################

executable               = /bioinfo/bin/interproscan
arguments                = -i input.fasta -b output_prefix

############################

queue