source: extensions/net.sf.basedb.genepattern/trunk/README @ 1138

Last change on this file since 1138 was 1138, checked in by Nicklas Nordborg, 14 years ago

References #223: Add target in build.xml for downloading required GenePattern? jar files

Now also downloads runVisualizer.jar. Added a separate ant script for downloading the same files as part of installing the package. Updated installation instructions.

File size: 6.0 KB
1== Requirements ==
3 1. BASE 2.13 or later.
4 2. Ant 1.7 or later (for installation only).
5 3. Access to a GenePattern server (3.2 or higher recommended).
7== Introduction ==
9This package is an extensions/plug-in package to BASE that integrates BASE
10with GenePattern. Some of the features:
12 * Export experimental data in various GenePattern file formats.
13 * Run jobs on a GenePattern server using files from BASE. Module
14   parameters are entered in the BASE web interface.
15 * Start GenePattern visualizer modules with files from BASE.
17This extension doesn't include any GenePattern software. It uses
18web services to communicate with GenePattern servers. BASE users
19that want to use GenePattern must have an account on a separate
20GenePattern server.
22For more information:
24 * The homepage for this extension:
26 * The GenePattern homepage:
29== Installation ==
31 1. Download the gp-integration-*.tar.gz file.
32 2. Unpack the downloaded file to a directory of your choice.
33 3. Download GenePattern files from a GenePattern server.
34    Type `ant -f download.xml`. This will dowload the files from the public
35    GenePattern server at You may
36    download from an alternate location by setting the `genepattern.url`
37    property: `ant -f download.xml -Dgenepattern.url=http://your.genepattern.server/gp`
38    This will download the following files.
39     * runVisualizer.jar: This file is added to gp-integration.jar/resources/visualizer
40     * The `GenePattern.jar` and `lib/gp-modules.jar` are extracted
41       to the `lib/genepattern` directory.
42 4. Copy the `gp-integration.jar` file and the `lib` directory, including sub-
43    directories and files, to your BASE extensions directory, `WEB-INF/extensions`.
44 5. Run the 'Extensions -> Manual scan' command if you have disabled automatic
45    installation. Otherwise, just wait a bit and the automatic installation will
46    find and install the new extension.
47 6. Run the plug-in installation wizard by clicking the 'New' button on the
48    'Administrate -> Plugins -> Definitions' page. Make sure the option for
49    the 'Extensions directory' is selected. Install all plug-ins found in
50    the gp-integration.jar file.
51 7. Done.
53== Using ==
55'''Register GenePattern account with BASE'''[[br]]
56BASE users that want's to use this extensions must have access to at
57least one GenePattern server. The first step is to register the account
58information with BASE. Go to `Extensions -> GenePattern options`. Add
59information for one or more GenePattern servers. For each server the
60following information should be provided:
62 * Server url: Only include the root url (not the /gp)
63 * Login: Your login information (email)
64 * Password: If the server requires a password
65 * BASE server URL: The URL to BASE as seen from the GenePattern server.
66   The default value is usually correct, but may need to be changed due
67   to, for example, proxies.
69Use the `Test` button to verify the login information. If there is problem with
70transfering files to the GenePattern server an incorrect value for the BASE server
71URL is most likely the cause.
73'''Configuring the GenePattern analysis plug-in'''[[br]]
74Before it is possible to run jobs on a GenePattern server the `GenePattern analysis`
75plug-in must be configured. Each GenePattern module requires a separate configuration.
76Go to the `Administrate -> Plugins -> Definitions` page and find the
77`GenePattern analysis` plug-in. Create a new configuration and start the
78configuration sequence.
80 1. In the first step you select a GenePattern server and a module. Use the
81    `Get list` button to retrieve a list of installed modules on the selected
82    GenePattern server. Note! The selected GenePattern server is used only
83    during configuration. Users may select a different server (as long as
84    the module is installed there) for executing jobs.
85 2. In the second step you can set default values for all non-file parameters
86    and link file parameters with BASE file types. The linking to file types
87    makes it possible for BASE to suggest a default file that is already
88    associated with the bioassay set.
90'''Using the GenePattern analysis plug-in'''[[br]]
91To run a job on a GenePattern server the `GenePattern analysis` plug-in is
92used from the bioassay set view.
94 1. In the first step some information about the new child bioassay set can
95    be entered. The user must also select a GenePattern server and specify
96    a directory in the BASE file system were the result files should be
97    saved.
98 2. In the second step input files and other parameter values are entered.
100To run a visualizer module, use the `GenePattern visualizer` button
101from the bioassay set view.
103 1. In the first step you select a GenePattern server and a module. Use the
104    `Get list` button to retreive a list of installed modules on the selected
105    GenePattern server.
106 2. In the second step input files and other parameter values are entered.
107 3. After this, the visualizer applet is started. This applet is just a wrapper
108    that downloads the required module and the data files to the local computer
109    and starts a Java program. Please be patient as this may take some while.
111== Known issues ==
115== Compiling ==
117To compile this package you also need:
119 1. Ant 1.7
120 2. Java 1.6
122Follow these instructions:
124 1. Download the source code from the subversion repository. See
126    for instructions.
128 2. Type `ant download-lib` to automatically download the BASE and GenePattern
129    files that are needed for compilation.
131 3. Type 'ant' to compile the code and generate the 'gp-integration.jar' file
132    in the project directory.
134 4. Use 'ant package' to create a downloadable tar.gz package. Note that this
135    package doesn't include any of the GenePattern files.
137Tip: If you need different values for any of the properties defined in
138the 'build.xml' file, create a file named '' and set
139the values there.
Note: See TracBrowser for help on using the repository browser.