source: extensions/net.sf.basedb.genepattern/trunk/README

Requirements

1. BASE 2.13 or later.
2. Ant 1.7 or later (for installation only).
3. Access to a GenePattern? server (3.2 or higher recommended).

Introduction

This package is an extensions/plug-in package to BASE that integrates BASE with GenePattern?. Some of the features:

• Export experimental data in various GenePattern? file formats.
• Run jobs on a GenePattern? server using files from BASE. Module parameters are entered in the BASE web interface.
• Start GenePattern? visualizer modules with files from BASE.

This extension doesn't include any GenePattern? software. It uses web services to communicate with GenePattern? servers. BASE users that want to use GenePattern? must have an account on a separate GenePattern? server.

For more information:

• The homepage for this extension: ​http://baseplugins.thep.lu.se/wiki/net.sf.basedb.genepattern
• The GenePattern? homepage: ​http://www.broad.mit.edu/cancer/software/genepattern/index.html

Installation

1. Download the gp-integration-*.tar.gz file.
2. Unpack the downloaded file to a directory of your choice.
3. Download GenePattern? files from a GenePattern? server. Type ant -f download.xml. This will dowload the files from the public GenePattern? server at ​http://genepattern.broad.mit.edu/gp. You may download from an alternate location by setting the genepattern.url property: ant -f download.xml -Dgenepattern.url=http://your.genepattern.server/gp This will download the following files.
   • runVisualizer.jar: This file is added to gp-integration.jar/resources/visualizer
   • GenePattern?.zip: The GenePattern.jar and lib/gp-modules.jar are extracted to the lib/genepattern directory.
4. Copy the gp-integration.jar file and the lib directory, including sub- directories and files, to your BASE extensions directory, WEB-INF/extensions.
5. Run the 'Extensions -> Manual scan' command if you have disabled automatic installation. Otherwise, just wait a bit and the automatic installation will find and install the new extension.
6. Run the plug-in installation wizard by clicking the 'New' button on the 'Administrate -> Plugins -> Definitions' page. Make sure the option for the 'Extensions directory' is selected. Install all plug-ins found in the gp-integration.jar file.
7. Done.

Using

Register GenePattern? account with BASE
BASE users that want's to use this extensions must have access to at least one GenePattern? server. The first step is to register the account information with BASE. Go to Extensions -> GenePattern options. Add information for one or more GenePattern? servers. For each server the following information should be provided:

• Server url: Only include the root url (not the /gp)
• Login: Your login information (email)
• Password: If the server requires a password
• BASE server URL: The URL to BASE as seen from the GenePattern? server. The default value is usually correct, but may need to be changed due to, for example, proxies.

Use the Test button to verify the login information. If there is problem with transfering files to the GenePattern? server an incorrect value for the BASE server URL is most likely the cause.

Configuring the GenePattern? analysis plug-in
Before it is possible to run jobs on a GenePattern? server the GenePattern analysis plug-in must be configured. Each GenePattern? module requires a separate configuration. Go to the Administrate -> Plugins -> Definitions page and find the GenePattern analysis plug-in. Create a new configuration and start the configuration sequence.

1. In the first step you select a GenePattern? server and a module. Use the Get list button to retrieve a list of installed modules on the selected GenePattern? server. Note! The selected GenePattern? server is used only during configuration. Users may select a different server (as long as the module is installed there) for executing jobs.
2. In the second step you can set default values for all non-file parameters and link file parameters with BASE file types. The linking to file types makes it possible for BASE to suggest a default file that is already associated with the bioassay set.

Using the GenePattern? analysis plug-in
To run a job on a GenePattern? server the GenePattern analysis plug-in is used from the bioassay set view.

1. In the first step some information about the new child bioassay set can be entered. The user must also select a GenePattern? server and specify a directory in the BASE file system were the result files should be saved.
2. In the second step input files and other parameter values are entered.

To run a visualizer module, use the GenePattern visualizer button from the bioassay set view.

1. In the first step you select a GenePattern? server and a module. Use the Get list button to retreive a list of installed modules on the selected GenePattern? server.
2. In the second step input files and other parameter values are entered.
3. After this, the visualizer applet is started. This applet is just a wrapper that downloads the required module and the data files to the local computer and starts a Java program. Please be patient as this may take some while.

Known issues

None.

Compiling

To compile this package you also need:

1. Ant 1.7
2. Java 1.6

Follow these instructions:

1. Download the source code from the subversion repository. See ​http://baseplugins.thep.lu.se/wiki/net.sf.basedb.genepattern for instructions.

2. Type ant download-lib to automatically download the BASE and GenePattern? files that are needed for compilation.

3. Type 'ant' to compile the code and generate the 'gp-integration.jar' file in the project directory.

4. Use 'ant package' to create a downloadable tar.gz package. Note that this package doesn't include any of the GenePattern? files.

Tip: If you need different values for any of the properties defined in the 'build.xml' file, create a file named 'build.properties' and set the values there.