InterProScan is developed to run on Linux. There are no versions planned for Windows or Apple (MAC OS X) operating systems. This is due to constraints in the various third-party binaries that InterProScan runs.
Note that InterProScan and the individual member database analyses are processor and memory intensive.
A minimum specification requirement is a machine with 2 cores and 4 GB of RAM, which will allow the analysis of a small number of sequences at a time. However the more resources the faster the analysis/more sequences can be analysed at a time.
- 64-bit Linux
- Perl 5 (default on most Linux distributions)
- Python 3 (InterProScan 5.30-69.0 onwards)
- Java JDK/JRE version 11 (InterProScan 5.37-76.0 onwards)
- Environment variables set
- $JAVA_HOME should point to the location of the JVM
- $JAVA_HOME/bin should be added to the $PATH
How to check these on a system?¶
Which version of Linux am I running?¶
InterProScan has been prepared with 64-bit binaries. To determine if you have a 32-bit or a 64-bit system, enter on the command line:
The exact response will depend upon the hardware vendor & architecture, however typical responses may look like:
64-bit as hinted by x86_64
$ uname -a Linux bob.com 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
32-bit as hinted by i686
$ uname -a Linux jim.com 2.6.32-50-generic-pae #112-Ubuntu SMP Tue Jul 9 20:44:31 UTC 2013 i686 GNU/Linux
If you are still in any doubt, ask your systems administrator.
Testing your Perl installation¶
To test that Perl 5 is installed, enter on the command line
This should report a version of Perl is available, similar to:
This is perl, v5.10.1 (*) built for i486-linux-gnu-thread-multi Copyright 1987-2009, Larry Wall ...etc
A default Perl installation is sufficient: no third party Perl modules need to be installed.
Alternatively you could change the value of the ‘perl.command’ property in your interproscan.properties configuration file to point at a suitable Perl installation, the default value is:
Testing your Python installation¶
To test that Python 3 is installed, enter on the command line
This should report a version of Python is available, similar to:
A default Python installation is sufficient: no third party Python modules need to be installed.
You could also change the value of the ‘python3.command’ property in your interproscan.properties configuration file to point at a suitable Python installation, the default value is:
Testing the Java environment¶
To test your environment, enter on the command line
This should report a version of java is available, similar to:
openjdk version "11.0.4" 2019-07-16 OpenJDK Runtime Environment AdoptOpenJDK (build 11.0.4+11) OpenJDK 64-Bit Server VM AdoptOpenJDK (build 11.0.4+11, mixed mode)
**InterProScan release 5.37-76.0 or later will only run with Java version 11.*++ **
You can get Java from many places. We have tested Java 11 from the OpenJDK Binaries from https://adoptopenjdk.net/ You can get information on OpenJDK reference implementations at https://jdk.java.net/ and download from https://openjdk.java.net/install/index.html
InterProScan releases prior to 5.37-76.0 required Java 8.
Appendix - Historical Java version testing information¶
Any Oracle/Open JDK/JRE with Java 1.8.x should work with InterProScan. Historical information about Java versions tested and confirmed to work/not work include below for information but this is not an exhaustive list!
Oracle JDK/JRE for InterProScan 5.17-56.0 or later
OpenJDK for Interproscan 5.17-56.0 or later
Oracle JDK/JRE for InterProScan 5.16-55.0 or before
OpenJDK for InterProScan 5.16-55.0 or before
|1.6.0_24||Linux (Red Hat Distribution)||x64||Doesn’t work||Reported by user|