InterProScan FTP site

Version 4.2

This is the FTP site for downloading InterProScan. During a typical installation you will need the following files:

Documentation

README giving a quick overview of how to use InterProScan and what the program actually does
Frequently Asked Questions for both the administrators and users (updated 15th March 2006)
Installation Instructions in txt format, should you wish to download InterProScan to your own server
Release Notes for the latest version of the software - what's new and what is coming soon.
Data Release Notes for the latest release of the data - which files have updated, etc.

Files on this site

ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/DATA/	Contains database files (2 tarballs)
ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/BIN/4.x/	Contains binaries pre-compiled for various OS
ftp://ftp.ebi.ac.uk/pub/databases/interpro/iprscan/RELEASE/latest/	Contains InterProScan itself (perl architecture) - currently v4.2, released November 2005

Please note that all files must be downloaded before Config.pl is run to do the installation.

Inter-release patches

Please check the PATCHES directory for patches and quick bug-fixes discovered since release. These will also be listed below, together with any changes required to the installation

The table below list patches since v4.2.

Date	File	Instructions
15 Mar 2006	SGE conf files	In v 4.2 of InterProScan, some of the SGE conf files have incorrect references to other files in them. Please ensure that all files referred to in sge6.conf exist by doing the following. Change: default.template=[%env IPRSCAN_HOME]/conf/sgeenv.sh default.tool.template=[%env IPRSCAN_HOME]/conf/sgetool.sh to: default.template=[%env IPRSCAN_HOME]/conf/sge6env.sh default.tool.template=[%env IPRSCAN_HOME]/conf/sge6tool.sh Please also ensure that the qstat_ipr.pl script exists in your iprscan/bin directory (if it is called qstat_ipr, rename file so that it matches in the sge6.conf file)
14 Mar 2006	prodom.ipr	Prodom.ipr was missing from the tar file. You may download it separately from the DATA directory (N.B. it is the same file as in release 12.0).
03 Mar 2006	fprintscan.conf	Edit the file iprscan/conf/fprintscan.conf and change the line beginning "cmdline=" so that it now reads cmdline= [%database] [%toolinput] -e [%evalue] -d 10 -E 257043 84355444 -fj -a -o 15 -M \| [%parser] -d [%parserdb]
03 Mar 2006	superfamily.conf	Edit the file iprscan/conf/superfamily.conf and change the line beginning "modelshmm=" so that it now reads modelshmm=[%env IPRSCAN_HOME]/data/superfamily.hmm
03 Mar 2006	hmmpfam.conf	Edit the file iprscan/conf/hmmpfam.conf and change the line "zvalue=7973" to zvalue=8183. Z-value is used when calculating e-values for the matches in HMMER searches; the new value is for the new Pfam 19 data.
03 Mar 2006	InterProScan.pm	Download this file into the directory iprscan/lib/Dispatcher/Tool/ . This is a fix for a bug in the processing of translated nucleotide sequences which meant that the last translated frame was always missed by mistake.
03 Mar 2006	PfamPostFilter.pm	Download this file into the directory iprscan/lib/Dispatcher/Tool/Hmmer/ . This is a change in the PostProcessing of Pfam results, needed with Pfam 19 data (released in InterPro v12.1)
22 Nov 2005	PfamPostFilter.pm	Download this file into the directory iprscan/lib/Dispatcher/Tool/Hmmer/ . This is a fix for a bug which meant that look-up of the Pfam short name did not work and as a consequence, the job failed
21 Nov 2005	InterProScan v 4.2 released

Apologies for any inconvenience these bugs may have caused