source: extensions/net.sf.basedb.genepattern/trunk/README @ 1104

Last change on this file since 1104 was 1104, checked in by Nicklas Nordborg, 13 years ago

References #224: Add a "Test" button on the GenePattern? 'edit server' page

The "Test" button is now in place. The installation may still be a bit messy since the GenePattern? jar files has to be manually installed. We need a way to figure out what to do about that. Another problem is that the default configuration of a GenePattern? server allows a user to login with any username. Non-existing accounts are automatically created and given server admin permissions! It is possible to lock this down, but there is no web interface for adminitration of GenePattern? user accounts. There is some documentation about this: http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_web_client.html#_Securing_the_Server

File size: 2.1 KB
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1== Requirements ==
2
3 1. BASE 2.12.1 or later.
4 
5== Introduction ==
6
7This package is an extension package to BASE that integrates BASE
8with GenePattern. .........
9
10For more information:
11
12 * The homepage for this extension:
13   http://baseplugins.thep.lu.se/wiki/net.sf.basedb.genepattern
14 * The GenePattern homepage: http://www.broad.mit.edu/cancer/software/genepattern/index.html
15
16== Installation ==
17
18 1. Download the gp-integration-*.tar.gz file.
19 2. Unpack the downloaded file to a directory of your choice.
20 3. Copy the `gp-integration.jar` file and the `lib` directory, including sub-
21    directories and files, to your BASE extensions directory, `WEB-INF/extensions`.
22 4. Run the 'Extensions -> Manual scan' command if you have disabled automatic
23    installation. Otherwise, just wait a bit and the automatic installation will
24    find and install the new extension.
25 5. Run the plug-in installation wizard by clicking the 'New' button on the
26    'Administrate -> Plugins -> Definitions' page. Make sure the option for
27    the 'Extensions directory' is selected. Install all plug-ins found in
28    the gp-integration.jar file.
29 6. TODO....
30 7. Done.
31
32
33== Known issues ==
34
35None.
36
37== Compiling ==
38
39To compile this package you also need:
40 
41 1. Ant 1.6
42 2. Java 1.6
43
44Follow these instructions:
45
46 1. Download the source code from the subversion repository. See
47    http://baseplugins.thep.lu.se/wiki/net.sf.basedb.genepattern
48    for instructions.
49 
50 2. Type `ant download-lib` to automatically download the BASE core JAR files that
51    are needed for compilation. You can also do this manually by copying the
52    BASE2Core.jar, BASE2Webclient.jar, BASE2CorePlugins.jar and BASE2WSClient.jar
53    from the BASE installation directory (<basedir>/www/WEB-INF/lib/) to the
54    ./lib/compile directory.
55
56 3. Type 'ant' to compile the code and generate the 'gp-integration.jar' file
57    in the project directory.
58
59 4. Use 'ant package' to create a downloadable tar.gz package.
60 
61Tip: If you need different values for any of the properties defined in
62the 'build.xml' file, create a file named 'build.properties' and set
63the values there.
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