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--- interproscan [2011/07/20 08:21] – aorth
+++ interproscan [2011/07/21 10:27] (current) – aorth
@@ Line 54: / Line 54: @@
 <code>yum list perl-</code>
-===== Accessing Interproscan =====
+==== Getting the files ====
-http://hpc.ilri.cgiar.org/iprscan/iprscan
+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>