Installation requirements¶
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.
Software requirements:
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:
uname -a
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
perl -version
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:
perl.command=perl
Testing your Python installation¶
To test that Python 3 is installed, enter on the command line
python3 --version
This should report a version of Python is available, similar to:
Python 3.5.1
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:
python3.command=python3
Testing the Java environment¶
To test your environment, enter on the command line
java -version
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 1.11.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
Version |
Build |
Operating System |
Architecture |
Status |
|---|---|---|---|---|
1.8.074 |
1.8.0_74-b02 |
Linux |
x64 |
Works |
1.8.060 |
1.8.0_60-b27 |
Linux |
x86 |
Works |
1.7.* |
Linux |
x86 |
Doesn’t work |
OpenJDK for Interproscan 5.17-56.0 or later
Version |
Operating System |
Architecture |
Status |
Misc |
|---|---|---|---|---|
1.8.0_66 |
Linux |
x64 |
Works |
|
1.7.* |
Linux |
x64 |
Doesn’t work |
Oracle JDK/JRE for InterProScan 5.16-55.0 or before
Version |
Build |
Operating System |
Architecture |
Status |
|---|---|---|---|---|
1.8.0 |
1.8.0-Works |
Linux |
x64 |
Doesn’t work |
1.7.0_51 |
1.7.0_51-b13 |
Linux |
x86 |
Works |
1.7.0_40 |
Linux |
x64 |
Works |
|
1.7.0 |
Linux |
x64 |
Works |
|
1.6.0_45 |
Linux |
x64 |
Works |
|
1.6.0_37 |
Linux |
x64 |
Works |
|
1.6.0_22 |
Linux |
x64 |
Works |
|
1.6.0_11 |
Linux |
x64 |
Works |
|
1.6.0_07 |
Linux |
x64 |
Works |
|
1.6.0_05 |
Linux |
x64 |
Works |
|
1.6.0_04 |
Linux |
x64 |
Works |
|
1.6.0_03 |
Linux |
amd64 |
Doesn’t work |
|
1.6.0_02 |
Linux |
amd64 |
Doesn’t work |
OpenJDK for InterProScan 5.16-55.0 or before
Version |
Operating System |
Architecture |
Status |
Misc |
|---|---|---|---|---|
1.7.0_25 |
Linux |
x64 |
Works |
:— |
1.6.0_30 |
Linux |
i686 |
Works |
:— |
1.6.0_27 |
Linux |
x64 |
Works |
:— |
1.6.0_24 |
Linux (Red Hat Distribution) |
x64 |
Doesn’t work |
Reported by user |