ILRI Research Computing

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===== Interproscan =====

Official FTP: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/

===== Installation =====
==== Requirements ====
From the readme, in addition to Bioperl, these packages must be installed on the head node and any compute nodes! Make sure they work!
<file>
1.1 Perl
The InterProScan package has been developed in Perl5 under UNIX and requires
that various perl modules be installed beforehand.  Please note that all these
modules are available via the CPAN website (http://search.cpan.org/)
  * DB_File.pm - the interface to Berkeley DB, which is a part of the standard Perl5 distribution.
  * XML::Parser.pm - libexpat (1.95.5 or newer) which is needed for the new implementation of
    BlastProDom and to parse xml outputs.
  * XML::Quote
  * English
  * File::Basename
  * File::Copy
  * File::Path
  * File::Spec::Functions
  * Sys::Hostname
  * Mail::Send
  * FileHandle
  * IO::Scalar
  * CGI
  * URI::Escape
  * IO::String</file>

Here is a script you can use to test if these modules are working on a particular node:
<file>#!/usr/bin/perl

use DB_File;
use XML::Parser;
use XML::Quote;
use English;
use File::Basename;
use File::Copy;
use File::Path;
use File::Spec::Functions;
use Sys::Hostname;
use Mail::Send;
use FileHandle;
use IO::Scalar;
use CGI;
use URI::Escape;
use IO::String;
use Bio::Perl;

exit;</file>
If it is successful you should not see any output.  Otherwise, you will have to install missing perl modules.  If you need to install perl modules you should probably check the system's package manager first, as that way the system will keep track of when there are updates, etc, as opposed to simply using CPAN or installing them manually.

List all perl modules available in yum:
<code>yum list perl-</code>

==== Getting the files ====
iprscan will unzip into its own folder, so you don't need to create one to hold all these files.  Just download them somewhere in your home directory:
<code>wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/RELEASE/latest/iprscan_v4.8.tar.gz
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/BIN/4.x/iprscan_bin4.x_Linux64.tar.gz
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/DATA/iprscan_DATA_33.0.tar.gz
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/DATA/iprscan_PTHR_DATA_31.0.tar.gz
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/DATA/iprscan_MATCH_DATA_33.0.tar.gz
</code>

==== Unzipping ====
<code>tar zxf iprscan_bin4.x_Linux64.tar.gz
tar zxf iprscan_DATA_33.0.tar.gz
tar zxf iprscan_MATCH_DATA_33.0.tar.gz
tar zxf iprscan_PTHR_DATA_31.0.tar.gz
tar zxf iprscan_v4.8.tar.gz</code>

==== Configuration ====
Create the destination directory and move the unzipped ''iprscan'' folder there.  The configuration script will want to know where you've put iprscan.
<code>sudo mkdir -p /export/apps/iprscan
sudo mv iprscan /export/apps/iprscan/4.8
cd /export/apps/iprscan/4.8
./Config.pl</code>
Wait a sec while it formats the databases...

==== Testing ====
<code>/export/apps/iprscan/4.8/bin/iprscan -cli -i /export/apps/iprscan/4.8/test.seq -o /tmp/iprscan_test.out -format raw -goterms -iprlookup</code>

==== Apache config ====
Paste the following in ///etc/httpd/conf.d/iprscan.conf//:
<file> Alias /doc/ "/export/apps/iprscan/4.8/doc/html/"
 Alias /images/ "/export/apps/iprscan/4.8/images/"
 Alias /tmp/ "/export/apps/iprscan/4.8/tmp/"

 ScriptAlias /iprscan/ "/export/apps/iprscan/4.8/bin/"

 <Directory "/export/apps/iprscan/4.8/images">
   Options Indexes MultiViews
   AllowOverride None
   Order allow,deny
   Allow from all
 </Directory>

 <Directory "/export/apps/iprscan/4.8/tmp/">
   Options FollowSymLinks Includes SymLinksIfOwnerMatch
    IndexIgnore */.??* *~ *# */HEADER* */README* */RCS
    AllowOverride AuthConfig Limit FileInfo

    Order deny,allow
    Deny from all
    Allow from .ilri.cgiar.org
 </Directory></file>
And then restart Apache with ''sudo apachectl graceful''.
=== Apache write permissions ===
Make sure Apache can write to the iprscan folder!
<code>sudo chown -R apache /export/apps/iprscan/4.8/</code>