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Interactive Display for Evolutionary Analyses

IDEA (Interactive Display for Evolutionary Analyses) is a graphical interface for PAML (Yang, Z., 1997), a popular package for conducting molecular evolution analyses on phylogenies and associated sequences.

http://ideanalyses.sourceforge.net/

Installation

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 here.

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!

Unpack the archive into a new folder:

  • $ mkdir idea
    $ cd idea
    $ tar zxf ../idea-2.4.4.tar.gz
    $ 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
    CheckAvailableMemory.java   idea                      idea_local_gene_template_user_tree.xml  jars               newickDraw        ss.make-idea-svg-graphs.pl
    check-java-memory           idea-A-create-tree.pl     idea_local_gene_template.xml            jdic               pdfbox            verify-java
    commons-io                  idea-B-run-paml.pl        idea_local_template.xml                 jdic-linux64       README            wf
    DEFAULT-BASEML.ctl          idea-C-merge-runs.pl      idea_template.xml                       jdic_stub.jar      RST.pm            Workflow
    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

Run the installer:

  • $ ./install-idea 
    Checking for required Perl modules...
    Unpacking wf-3.1.1.tar.gz...
    Using grid type sge!
    Configuring Workflow...
    Unpacking jruby-bin-1.0.0RC1.tar.gz...
    Checking for required PHYLIP programs...
    Checking for required PAML programs...
    Checking for other required programs...
    Unpacking PDFBox-0.7.2.zip...
    Unpacking jdic-20060613-bin-cross-platform.zip...
    Unpacking xstream-distribution-1.2.1-src.zip...
    Configuring IDEA...
    Compiling...
    Congratulations!  You have successfully installed IDEA.
    You may find it convenient to add /export/home/alan/idea to your path for easy access to IDEA.
    
    SGE event logs will be stored in /export/home/alan/idea/wf/event-logs.
    This directory should be cleaned out periodically.
    The script delete-old-event-logs may be used for this purpose.
    
    NOTICE TO SGE (SUN GRID ENGINE) USERS:
    ======================================
    IDEA uses the Workflow process management system to manage grid submissions.
    In order to work with SGE, Workflow requires the following set-up by a grid administrator:
    The scripts /export/home/alan/idea/wf/bin/prolog_uninitialized and /export/home/alan/idea/wf/bin/epilog_uninitialized must be installed as prolog and epilog, respectively, on every queue on which Workflow jobs will be executed.
    
    Grid submissions have been temporarily disabled.
    You may still use IDEA, but all processes will be executed on the machine from which you launch IDEA.
    
    Once an administrator has installed these scripts, rename /export/home/alan/idea/wf/bin/prolog_uninitialized to /export/home/alan/idea/wf/bin/prolog and /export/home/alan/idea/wf/bin/epilog_uninitialized to /export/home/alan/idea/wf/bin/epilog to enable grid submissions.
    
    (If Workflow has already been installed on your grid, prolog and epilog do not need to be reinstalled.)

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.

  • $ grep -rl home/alan * | xargs sed -i 's/home\/alan/paracel\/biosoft/g'

Copy the directory to somewhere more appropriate (using sudo because it's outside of our home):

  • $ cd ..
    $ sudo cp -R idea /export/paracel/biosoft/

Change everything to 777 permissions, this allows idea to run just fine, but is very insecure:

$ sudo chmod -R 777 /export/paracel/biosoft/

Add the installed directory to your shell's path so you can test it:

  • $ export PATH=/export/paracel/biosoft/idea:${PATH}
idea.txt · Last modified: 2010/05/22 17:19 (external edit)