InterProScan
Overview
InterProScan is the software package that allows sequences to be scanned against InterPro’s member database signatures.
Version 5.48-83.0 is installed on the CSF.
Please note that the Pre-calculated match lookup service is not enabled – all results will be calculated on the CSF.
The initial_setup.py script has been run to index the data files.
Restrictions on use
There are no restrictions on accessing the software on the CSF. It is distributed under the open source Apache License , as are the included scanning tools (except SignalP and TMHMM) and all usage must adhere to that license.
Set up procedure
We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.
Load one of the following modulefiles:
module load apps/binapps/interproscan/5.48-83.0
Test Data
You can now copy the test files from the installation to your current directory if you wish to run some test jobs:
cp $IPS_HOME/test* $PWD
Running the application
Please do not run InterProScan on the login node. Jobs should be submitted to the compute nodes via batch.
You may run the following to obtain help on the command-line flags:
module load apps/binapps/interproscan/5.48-83.0 qrsh l short -V -pe smp.pe 2 interproscan.sh --help
Serial batch job submission
Serial jobs are not supported. You will need at least 2 CPU cores to run InterProScan. An example of a parallel jobscript is given below.
If you need more RAM (memory) to complete the analysis successfully, and you may well do!, please add the flags mentioned at the high-memory jobs page for more information.
Parallel batch job submission
Create a batch submission script (which will load the modulefile in the jobscript), for example:
#!/bin/bash --login #$ -cwd # Job will run from the current directory #$ -pe smp.pe 16 # Number of cores, can be 2--32 ### You may need to add a high memory flag here (see above) # Choose your required version module load apps/binapps/interproscan/5.48-83.0 # $NSLOTS is automatically set to the number of cores requested above interproscan.sh -T ~/scratch -cpu $NSLOTS options...
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.