Differences

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--- interproscan [2010/05/22 14:19] – external edit 127.0.0.1
+++ interproscan [2011/07/21 10:27] (current) – aorth
@@ Line 1: / Line 1: @@
 ===== Interproscan =====
-Change EBI logo to ILRI logo on wait page?
+Official FTP: ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/
-http://hpc.ilri.cgiar.org/iprscan/iprscan
 ===== Installation =====
@@ Line 52: / Line 49: @@
 exit;</file>
-Run it on a node like this:
+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.
-<code>$ rocks run host compute-0-16 'perl scripts/testperl.pl'
+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>
-If it is successful you should not see any output.
-==== Accessing Interproscan ====
+==== Unzipping ====
-http://hpc.ilri.cgiar.org/iprscan/iprscan
+<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>