Changeset 125

Jul 20, 2006, 10:04:07 AM (16 years ago)
Jari Häkkinen

Continued improving docs.

1 added
4 edited


  • trunk/se/lu/thep/affymetrix/INSTALL

    r124 r125  
    6464G4, and SuSE Linux (v10).
     66You should install the RMAExpressConsole binary such that it is
     67readable for the user running your BASE application server. Remember
     68this location for configuration of BASE below.
    6670Install of the plug-in will succeed even if this requisite is not
    6771fulfilled, but execution of the plug-in will fail.
    85893. Installation
    87 v) Install the plug-in in the server file system.
     91v) Install the plug-in in the BASE application server file system.
    8993  make BASEDIR=<base-dir> install
    9195where <base-dir> is to be replaced by the path to BASE. The plug-in
    9296will install in the recommended directory
    93 <base-dir>/plugins/se/lu/thep/RMAExpress, i.e. if you prefer another
     97<base-dir>/plugins/se/lu/thep/affymetrix, i.e. if you prefer another
    9498location you need to change the Makefile.
     100For advanced users only: <base-dir> can really be any directory
     101readable for the user running your tomcat server. This may be handy if
     102you run several servers on one machine but only want one common
     103directory hierarchy for the plug-ins. Or, if you update the BASE
     104application frequently and in the process create new directories for
     105the newer core.
     107 Remember this location for configuration of BASE below.
    971104. BASE configuration
    99 vi) Make BASE aware of the new plug-in ... to be written.
     112vi) Make BASE aware of the new plug-in:
     114 - Login to BASE with plug-in administrative privileges.
     115 - Choose 'Administrate' -> 'Plugins' -> 'Definitions'.
     116 - Click on 'New...'. This will open up the 'Create plugin' pop-up
     117   window. Type "" in the 'Class'
     118   field and "<base-dir>/plugins/se/lu/thep/affymetrix/RMAExpress.jar"
     119   in the 'Path' field. Replace <base-dir> with whatever you used in
     120   item 3.v) above.
     121 - Locate 'RMAExpress plug-in' in the list of plug-in and click on
     122   it. On the page that appears, click 'New Configuration ...' and a
     123   'Create configuration' pop-up will appear. Type an appropriate name
     124   in the 'Name' field and click on the 'Save and configure' button.
     125 - There is only one configuration option to set in the 'Configure
     126   plugin' pop-up, the name and location of the RMAExpressConsole
     127   binary. Click on the required option 'RMAExpressConsole ...' and
     128   type the full path to the RMAExpressConsole binary from item 1.ii)
     129   above.
     1315. That's it, now you need to BASE skills to actually make use of the
     132   RMAExpress plug-in. Read the README file for some pointers on what
     133   to do now.
  • trunk/se/lu/thep/affymetrix/Makefile

    r124 r125  
    2828JAR  = RMAExpress.jar
    30 BINDISTFILES = Changelog INSTALL Makefile README RMAExpress.jar
     30BINDISTFILES = Changelog COPYING INSTALL Makefile README RMAExpress.jar
    3131VERSION = pre0.1
    3232PACKAGEFILE = base_rmaexpress_plugin-$(VERSION)
  • trunk/se/lu/thep/affymetrix/README

    r124 r125  
    55 What is required to use the RMAExpress for BASE plug-in?
     55What is required to use the RMAExpress plug-in for BASE?
    57 1) You need to install the plug-in, see INSTALL for instruction on how
    58    to preform installation of this plug-in.
     571) You need to install the plug-in and make BASE aware of the new
     58   plugin, see INSTALL for instruction for installation
     59   instructions.
    60612) You need to import probe set information into BASE (reporter
    61    information), i.e. import AffyChip_annot.csv into BASE.
     62   information), i.e. import AffyChip_annot.csv into BASE. This is
     63   only needed to do once, and optionally later if reporter
     64   information should be updated. This must be performed by a user
     65   with reporter administrative privilieges, an ordinary BASE user do
     66   NOT have this privilege.
     68   - First you need to create an plug-in configuration for the
     69     'Reporter importer' plug-in. Locate the 'Reporter importer'
     70     plug-in definition ('Administrate' -> 'Plugins' ->
     71     'Definitions'). Click on it and choose 'New configuration ...',
     72     name the configuration and choose 'Save and configure'.
     74   - A 'Parser settings' dialog will appear. Set fields according to
     75     this list:
     77       Data header  : "Probe Set ID","GeneChip Array",.*
     78       Data splitter: (?!"),(?=")
     79       Remove quotes: true
     80       Name         : \Probe Set ID\
     81       Reporter ID  : \Probe Set ID\
     83    Finalize by clicking 'Next'.
     85   - Import the reporters by choosing 'View' -> 'Reporters' and the
     86     clicking on 'Import...'. Click 'Next' without changing the 'auto
     87     detect' settings. Supply the filename in the next dialog, click
     88     'Next'. Start the import by clicking 'Next' in the parameter
     89     dialog.
    63913) You need to define the design of the AffyChip in BASE, i.e. import
  • trunk/se/lu/thep/affymetrix/

    r123 r125  
    184184        Request.COMMAND_CONFIGURE_PLUGIN,
    185185        "Configure plugin",
    186         "The executable for RMAExpressConsole",
     186        "Set the path to the RMAExpressConsole executable",
    187187        parameters);
    188188    }
    422422    ("RMAExpress plug-in", "Computes gene expression summary values for " +
    423423     "Affymetrix Genechip data using the Robust Multichip Average " +
    424      "expression summary", "$Revision$ $Date$",
    425      "2006 Jari Häkkinen, Department of Theoretical Physics, Lund University",
     424     "expression summary", "$Revision$ $Date$","2006 Jari H&auml;kkinen, " +
     425     "Department of Theoretical Physics, Lund University",
    426426     null, "", "" );
    427427  private RequestInformation configureJob = null;
    428428  private RequestInformation configurePlugin = null;
    429429  private static PluginParameter<String> execPathParameter =
    430     new PluginParameter<String>("execPath","RMAExpressConsole executables path",
     430    new PluginParameter<String>("execPath","RMAExpressConsole executable",
    431431                                "The path to the executable",
    432432                                new StringParameterType(255, null, true));
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