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