Obtaining a copy of InterProScan¶
Firstly check your system satisfies the Installation requirements. To install the InterProScan 5 software you then need to complete the following steps:
Install the core InterProScan
Configure the Pre-calculated Match Lookup
Obtaining the core InterProScan software¶
mkdir my_interproscan
cd my_interproscan
wget https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.67-99.0/interproscan-5.67-99.0-64-bit.tar.gz
wget https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.67-99.0/interproscan-5.67-99.0-64-bit.tar.gz.md5
# Recommended checksum to confirm the download was successful:
md5sum -c interproscan-5.67-99.0-64-bit.tar.gz.md5
# Must return *interproscan-5.67-99.0-64-bit.tar.gz: OK*
# If not - try downloading the file again as it may be a corrupted copy.
(Direct link: https://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.67-99.0/interproscan-5.67-99.0-64-bit.tar.gz)
As the compressed file is large, it is strongly recommended that you use md5sum to check that the file has been downloaded without errors, as described above.
Extract the tar ball:
tar -pxvzf interproscan-5.67-99.0-*-bit.tar.gz
# where:
# p = preserve the file permissions
# x = extract files from an archive
# v = verbosely list the files processed
# z = filter the archive through gzip
# f = use archive file
This is a completely self-contained version that includes member database specific binaries and model / signature files. This should run ‘out of the box’ on a Linux system. Note that it excludes analyses that contain components for which you are obliged to acquire your own license.
Index hmm models¶
Before you run interproscan for the first time, you should run the command:
python3 setup.py -f interproscan.properties
This command will press and index the hmm models to prepare them into a format used by hmmscan.
Panther models¶
Previous versions of InterProScan required a separate installation of Panther data. Starting with InterProScan 5.47-82.0 onwards, this is not necessary. Panther data is bundled together with the rest of the application data.
Using the Local Pre-calculated Match Lookup Service (optional)¶
This service is by default switched on, so you don’t need to do any more installation or configuration, unless you want to install your own Pre-calculated Match Lookup Service. The uncompressed Match Lookup Service disk usage comes to more that 1TB, so it is recommended just to use the default setup.
The pre-calculated match lookup web service is able to provide matches to more than 500 million protein sequences, including all of the sequence in UniProtKB.
By default InterProScan is configured (in the interproscan.properties file) to use the web service hosted at the EBI. Your servers will need to have external access to http://www.ebi.ac.uk to use it.
InterProScan uses this service to retrieve pre-calculated matches, reducing the need for compute on your server and speeding up the response time.
If you are behind a firewall that prevents such access and you are unable to configure access, you could either Installing the lookup service locally or turn off the use of this service, which means the analysis will run locally without any match lookup
To turn off the use of the service, either use the -dp command line option or edit interproscan.properties and add a # to the start of the following line to comment out the line or delete the following line, near the bottom of the file:
precalculated.match.lookup.service.url=http://www.ebi.ac.uk/interpro/match-lookup
It is important to note that we run the latest available version of the pre-calculated match lookup service at the EBI. In the event of a new release, you will be required to either install the latest version of InterProScan 5, or to install the required version of the lookup service locally :ref:`The InterProScan Lookup Match Service.