Changeset 1138


Ignore:
Timestamp:
Jun 24, 2009, 12:50:39 PM (13 years ago)
Author:
Nicklas Nordborg
Message:

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.

Location:
extensions/net.sf.basedb.genepattern/trunk
Files:
1 added
4 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.genepattern/trunk/README

    r1117 r1138  
    22
    33 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).
    46 
    57== Introduction ==
    68
    7 This package is an extension package to BASE that integrates BASE
    8 with GenePattern. .........
     9This package is an extensions/plug-in package to BASE that integrates BASE
     10with GenePattern. Some of the features:
     11
     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.
     16
     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.
    921
    1022For more information:
     
    1224 * The homepage for this extension:
    1325   http://baseplugins.thep.lu.se/wiki/net.sf.basedb.genepattern
    14  * The GenePattern homepage: http://www.broad.mit.edu/cancer/software/genepattern/index.html
     26 * The GenePattern homepage:
     27   http://www.broad.mit.edu/cancer/software/genepattern/index.html
    1528
    1629== Installation ==
     
    1831 1. Download the gp-integration-*.tar.gz file.
    1932 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-
     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 http://genepattern.broad.mit.edu/gp. 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     * GenePattern.zip: 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-
    2143    directories and files, to your BASE extensions directory, `WEB-INF/extensions`.
    22  4. Run the 'Extensions -> Manual scan' command if you have disabled automatic
     44 5. Run the 'Extensions -> Manual scan' command if you have disabled automatic
    2345    installation. Otherwise, just wait a bit and the automatic installation will
    2446    find and install the new extension.
    25  5. Run the plug-in installation wizard by clicking the 'New' button on the
     47 6. Run the plug-in installation wizard by clicking the 'New' button on the
    2648    'Administrate -> Plugins -> Definitions' page. Make sure the option for
    2749    the 'Extensions directory' is selected. Install all plug-ins found in
    2850    the gp-integration.jar file.
    29  6. TODO....
    3051 7. Done.
    3152
     53== Using ==
     54
     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:
     61
     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.
     68
     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.
     72
     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.
     79
     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.
     89
     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.
     93
     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.
     99
     100To run a visualizer module, use the `GenePattern visualizer` button
     101from the bioassay set view.
     102
     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.
    32110
    33111== Known issues ==
     
    39117To compile this package you also need:
    40118 
    41  1. Ant 1.6
     119 1. Ant 1.7
    42120 2. Java 1.6
    43121
     
    48126    for instructions.
    49127 
    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.
     128 2. Type `ant download-lib` to automatically download the BASE and GenePattern
     129    files that are needed for compilation.
    55130
    56131 3. Type 'ant' to compile the code and generate the 'gp-integration.jar' file
    57132    in the project directory.
    58133
    59  4. Use 'ant package' to create a downloadable tar.gz package.
     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.
    60136 
    61137Tip: If you need different values for any of the properties defined in
  • extensions/net.sf.basedb.genepattern/trunk/build.xml

    r1117 r1138  
    5959        prefix="${tar.prefix}"
    6060        preserveLeadingSlashes="true"
    61         includes="${jar.name},README,LICENSE*,lib/genepattern/*"
     61        includes="${jar.name},download.xml,README,LICENSE*,lib/genepattern/*"
    6262        excludes="lib/genepattern/GenePattern.jar,lib/genepattern/gp-modules.jar"
    6363        >
     
    8080      >
    8181      <fileset dir="${build}" />
    82       <fileset dir="." includes="resources/**" />
     82      <fileset dir="." includes="resources/**"
     83        excludes="resources/visualizer/runVisualizer.jar"/>
    8384    </jar>
    8485  </target>
     
    142143    <download-lib file="BASE2WSClient.jar" />
    143144    <!-- We only need some files from the GenePattern.zip file -->
     145    <download-lib file="runVisualizer.jar" todir="./resources/visualizer" from="${genepattern.jars}" />
    144146    <download-lib file="GenePattern.zip" todir="${build}" from="${genepattern.jars}" />
    145147    <unzip dest="lib/genepattern" src="${build}/GenePattern.zip">
     
    150152      <mapper type="flatten"/>
    151153    </unzip>
     154    <delete file="${build}/GenePattern.zip" />
    152155  </target>
    153156 
  • extensions/net.sf.basedb.genepattern/trunk/lib/genepattern

    • Property svn:ignore
      •  

        old new  
        1 *.jar
         1GenePattern.jar
         2gp-modules.jar
  • extensions/net.sf.basedb.genepattern/trunk/resources/visualizer

    • Property svn:ignore set to
      runVisualizer.jar
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