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--- interproscan [2009/09/11 06:27] – created 172.26.0.166
+++ interproscan [2011/07/20 08:21] – aorth
@@ Line 1: / Line 1: @@
-====== Interproscan ======
+===== Interproscan =====
-Check configuration to use LSF.
-Download and install lates databases
+Change EBI logo to ILRI logo on wait page?
-Change EBI logo to ILRI logo
+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 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>
+===== Accessing Interproscan =====
+http://hpc.ilri.cgiar.org/iprscan/iprscan