Interproscan
Description
InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.
License
The InterProScan software is distributed under the open source Apache license, as are the included scanning tools (except SignalP and TMHMM). Therefore, you do not need a special license for commercial use but please cite the resource and keep the Copyright statement with your installation.
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of interproscan and load default version of interproscan as
module avail interproscan/ # list available modules module load interproscan # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail interproscan
and choose explicit version you want to use. and run Interproscan with -T parameter
interproscan.sh -T $SCRATCHDIR ...
By parameter -T is set temporary directory instead of /temp to $SCRATCHDIR (available disk space in /temp is limited). To use this parameter you must request a scratch in job's requirements. Argument -i is path to fasta file that should be loaded.
A number of used processors (workers) is set in the file interproscan.properties to 8, so with one master you should request for 9-10 CPUs.
Documentation
- http://www.ebi.ac.uk/interpro/interproscan.html
- https://www.ebi.ac.uk/interpro/about.html
- IterProScan 5 user's guide https://github.com/ebi-pf-team/interproscan/wiki