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APBioBox - Bioinformatics in a box!

APBioBox Release 1.0 Beta1

Table of Contents

 

What is APBioBox?

APBioBox bundles various cool stuff of bioinformatics and provides a grid framework for integration with APBioGrid. The components of APBioBox are classified into the following groups:

  1. bio-applications,
  2. grid middleware,
  3. workflow engine for bio-apps, and
  4. bio-databases (which is under development as it is).

APBioBox is a project by Asia Pacific Bioinformatics Network under the funding of International Research and Development Council (IDRC) of Canada. The software developed in this project is free for distribution under the GPL open source model. However, the packages being bundled are under their respective licensing terms.

In this release, the following components are included:

  1. Globus Toolkit 2.4 - grid middleware
  2. KOOPlatform 3 client - workflow builder and executor
  3. Bio applications:
    • abacus-0.63
    • blast-2.2.5
    • mgalign-linux-1.3.6
    • clustalw-1.83
    • tv-0.3
    • emboss-2.7.1
    • embassy-hmmer-2.1.1
    • embassy-phylip-3.573c
    • embassy-sim4-1.0.0
    • wise-2.2.0
    • fasta3-3.4

 

Requirements to install and run APBioBox

Currently only one platform is supported, which is Redhat 9. It should be able to run on Redhat 7.3 and Redhat 8, but we need to work on some of the dependency issues first. We have plans to port to other platforms in time to come. Any offer of assistance in any form (manpower, test platform, monetary and consulting) is most welcome.

On Redhat 9, it is recommended that the target system is installed using "Server" install option, with the X Windows selected.

Java 1.4.1, which is bundled here, is required to install and run the KOOPlatform workflow client. If you have other version, you may have problem with the Java Webstart.

Upon installation, some shortcuts pointing to APBioBox programs will appear if the windows desktop used is GNOME or KDE. The shortcuts should also appear on windows desktop which follow the specifications of the OpenDesktop group.

 

How to Install

To install APBioBox, do the following as root: 

	# tar -xzf apbiobox-xxx-xxx.tar.gz
	# cd apbiobox-xxx-xxx
	# ./install.sh

install.sh is the "meta-installer" which will take care of the installation of all APBioBox components. It always installs into $APBIOBOX_LOCATION, which is currently set to /usr/apbiobox. If you would like to install APBioBox somewhere else, create a symbolic link of /usr/apbiobox pointing it to the target directory.

To create a symbolic link to your target directory, do the following as root: 

	# ln -s /usr/apbiobox <my.apbiobox.dir>

See the following section "Share Your Resource" for alternate installation mode.

The installation takes three minutes or more to complete depending on the hardware capabilities.

After the installation, you need to perform the following steps manually:

  1. Request for a host cert for your newly installed system/grid node
    • Copy the content of /etc/grid-security/hostcert_request.pem and email it to grid-ca@apbionet.org as it is, from a valid email account.
    • A host cert will be issued by the APBioGrid CA and emailed to you.
    • Copy the cert content into /etc/grid-security/hostcert.pem.
    • Run $APBIOBOX_LOCATION/gt-2.4/setup/globus/setup-globus-gram-job-manager

 

Share Your Resource

APBioBox provides the collaborative framework by participating in the APBioGrid. By default, APBioBox is installed in "register-only" mode, i.e. it only registers the installation and resources available to the APBioGrid MDS (the directory service). However, if you are running a non-critical system and/or wish to share your resource, you can install using "share" mode. "Share" mode will allow access to your resources through a common, controlled certificate managed by APBioGrid. This is a way to contribute to the community or experiment with the grid services.

To install your APBioBox in "share" mode, do the following as root: 

	# tar -xzf apbiobox-xxx-xxx.tar.gz
	# cd apbiobox-xxx-xxx
	# ./install.sh -share

A login account "apbiobox" is automatically created for "share" mode. This account is used to run processes launched through the common certificate.

In technical terms, "share" mode installation adds an entry into /etc/grid-security/grid-mapfile.

 

How to Uninstall

An uninstaller is provided. To uninstall APBioBox, do the following: 

	# cd $APBIOBOX_LOCATION
	# ./uninstall.sh

 

How to use APBioBox

There are two ways to run the executables:

  1. Packages are installed into their respective subdirectory. Usually the executables are stored in bin and sbin subdirectories.
  2. All executables of APBioBox are symbolically linked from $APBIOBOX_LOCATION/bin. You can set your PATH to include this directory and you should immediately have access to all APBioBox executable.

    Note: Some executables may not work properly through the symbolic links.

To run the KOOPlatform workflow client, execute $APBIOBOX_LOCATION/bin/koopclient.sh in your X Windows.

To run the KOOPlatform daemon agent, execute $APBIOBOX_LOCATION/bin/koopdaemon.sh in your X Windows.

Optionally, you can click on the KOOPClient and/or KOOPDaemon icon on your desktop.

To perform tasks related to grid using Globus Toolkit, read 00-GLOBUS_GUIDE.

 

 

 

 

Updated Oct; July; Apr 2004; 4 Dec 2003 (ttw); 16 Sep 2003 - ogs