Differences

This shows you the differences between two versions of the page.

--- idea [2009/08/19 08:04] – alan
+++ idea [2010/05/22 14:19] (current) – external edit 127.0.0.1
@@ Line 9: / Line 9: @@
 These notes were made when the HPC was running Rocks 4.1, so they may or may not work the same way after the cluster is upgraded to Rocks 5.2.  You may find want to make sure the pre-requisites are installed before going on.  The IDEA website has documentation but the installation literature is VERY limited!  The documentation for downloading and installing is on IDEA's sourceforge website [[http://ideanalyses.sourceforge.net/download_idea.html#sysreq|here]].
-<note warning>For whatever reasons, the installer is a bit picky, so **don't run it as root**!  We "install" it in a regular user's home folder first, and then later move it to another location where other users can use it.  Remember, don't use ''sudo'' to run the installer script!</note>
+<note warning>For whatever reasons, the installer is a bit picky, so **don't run it as root**!  We "install" it in a regular user's home folder first, and then move it to another location where other users can use it.  Remember, don't use ''sudo'' to run the installer script!</note>
-  * Unpack the archive into a new folder:
+Unpack the archive into a new folder:
-<code>[alan@hpc-ilri: ~]$ mkdir idea
+  * <code>$ mkdir idea
-[alan@hpc-ilri: ~]$ cd idea
+$ cd idea
-[alan@hpc-ilri: ~/idea]$ tar zxf ../idea-2.4.4.tar.gz
+$ tar zxf ../idea-2.4.4.tar.gz
-[alan@hpc-ilri: ~/idea]$ ls
+$ ls
 apache-batik                docs                      idea_gene_template_user_tree.xml        #install-idea.pl#  log4j.properties  source
 CheckAvailableMemory.class  external-docs             idea_gene_template.xml                  install-idea.pl    Logger.pm         ss.convert-svg-files.pl
@@ Line 24: / Line 24: @@
 DEFAULT-CODEML.ctl          idea_config_skeleton.ini  install-idea                            jruby              rubylib           xstream
 delete-old-event-logs       idea-D-parse-output.pl    install-idea.bash                       LICENSE            SeqGraph</code>
-  * Run the installer:
+Run the installer:
-<code>[alan@hpc-ilri: ~/idea]$ ./install-idea
+  * <code>$ ./install-idea
 Checking for required Perl modules...
 Unpacking wf-3.1.1.tar.gz...
@@ Line 59: / Line 59: @@
 (If Workflow has already been installed on your grid, prolog and epilog do not need to be reinstalled.)</code>
 The program has a funny installer, as the software package isn't really "installed" (it's more like "configured").  This has the unfortunate side effect of putting lots of static references to the user's home directory where it was "installed."
-  * Replace all instances of "home/alan" with "paracel/biosoft" so that the program runs correctly when we move it to its new location.
-<code>[alan@hpc-ilri: ~/idea]$ grep -rl home/alan * | xargs sed -i 's/home\/alan/paracel\/biosoft/g'</code>
+Replace all instances of "home/alan" with "paracel/biosoft" so that the program runs correctly when we move it to its new location.
-  * Copy the directory to somewhere more appropriate (using ''sudo'' because it's outside of our home):
+  * <code>$ grep -rl home/alan * | xargs sed -i 's/home\/alan/paracel\/biosoft/g'</code>
-<code>[alan@hpc-ilri: ~/idea]$ cd ..
+Copy the directory to somewhere more appropriate (using ''sudo'' because it's outside of our home):
-[alan@hpc-ilri: ~]$ sudo cp -R idea /export/paracel/biosoft/</code>
+  * <code>$ cd ..
-  * Add the installed directory to your shell's path so you can execute it from anywhere:
+$ sudo cp -R idea /export/paracel/biosoft/</code>
-<code>[alan@hpc-ilri: ~/idea]$ export PATH=${PATH}:/export/paracel/biosoft/idea</code>
+Change everything to 777 permissions, this allows idea to run just fine, but is very insecure:
+<code>$ sudo chmod -R 777 /export/paracel/biosoft/</code>
+Add the installed directory to your shell's path so you can test it:
+  * <code>$ export PATH=/export/paracel/biosoft/idea:${PATH}</code>