| 1 | == Requirements == |
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| 2 | |
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| 3 | 1. BASE 2.12.0 or later. |
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| 4 | |
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| 5 | == Introduction == |
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| 6 | |
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| 7 | This package is an extension package to BASE that integrates BASE |
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| 8 | with GenePattern. ......... |
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| 9 | |
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| 10 | For more information: |
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| 11 | |
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| 12 | * The homepage for this extension: |
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| 13 | http://baseplugins.thep.lu.se/wiki/net.sf.basedb.genepattern |
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| 14 | * The GenePattern homepage: http://www.broad.mit.edu/cancer/software/genepattern/index.html |
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| 15 | |
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| 16 | == Installation == |
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| 17 | |
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| 18 | 1. Download the gp-integration-*.tar.gz file. |
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| 19 | 2. Unpack the downloaded file to a directory of your choice. |
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| 20 | 3. Copy the gp-integration.jar file to your BASE extensions directory: |
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| 21 | WEB-INF/extensions. |
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| 22 | 4. Run the 'Extensions -> Manual scan' command if you have disabled automatic |
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| 23 | installation. Otherwise, just wait a bit and the automatic installation will |
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| 24 | find and install the new extension. |
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| 25 | 5. Run the plug-in installation wizard by clicking the 'New' button on the |
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| 26 | 'Administrate -> Plugins -> Definitions' page. Make sure the option for |
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| 27 | the 'Extensions directory' is selected. Install all plug-ins found in |
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| 28 | the gp-integration.jar file. |
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| 29 | 6. TODO.... |
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| 30 | 7. Done. |
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| 31 | |
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| 32 | |
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| 33 | == Known issues == |
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| 34 | |
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| 35 | None. |
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| 36 | |
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| 37 | == Compiling == |
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| 38 | |
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| 39 | To compile this package you also need: |
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| 40 | |
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| 41 | 1. Ant 1.6 |
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| 42 | 2. Java 1.6 |
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| 43 | |
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| 44 | Follow these instructions: |
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| 45 | |
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| 46 | 1. Download the source code from the subversion repository. See |
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| 47 | http://baseplugins.thep.lu.se/wiki/net.sf.basedb.genepattern |
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| 48 | for instructions. |
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| 49 | |
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| 50 | 2. Type `ant download-lib` to automatically download the BASE core JAR files that |
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| 51 | are needed for compilation. You can also do this manually by copying the |
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| 52 | BASE2Core.jar, BASE2Webclient.jar, BASE2CorePlugins.jar and BASE2WSClient.jar |
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| 53 | from the BASE installation directory (<basedir>/www/WEB-INF/lib/) to the |
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| 54 | ./lib/compile directory. |
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| 55 | |
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| 56 | 3. Type 'ant' to compile the code and generate the 'gp-integration.jar' file |
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| 57 | in the project directory. |
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| 58 | |
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| 59 | 4. Use 'ant package' to create a downloadable tar.gz package. |
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| 60 | |
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| 61 | Tip: If you need different values for any of the properties defined in |
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| 62 | the 'build.xml' file, create a file named 'build.properties' and set |
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| 63 | the values there. |
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