Changeset 125

Timestamp:

Jul 20, 2006, 10:04:07 AM (17 years ago)

Author:

Jari Häkkinen

Message:

Continued improving docs.

Location:

trunk/se/lu/thep/affymetrix

Files:

• COPYING (added)
• INSTALL (modified) (3 diffs)
• Makefile (modified) (1 diff)
• README (modified) (1 diff)
• RMAExpress.java (modified) (2 diffs)

trunk/se/lu/thep/affymetrix/INSTALL

@@ -64 +64 @@
 G4, and SuSE Linux (v10).
 
+You should install the RMAExpressConsole binary such that it is
+readable for the user running your BASE application server. Remember
+this location for configuration of BASE below.
+
 Install of the plug-in will succeed even if this requisite is not
 fulfilled, but execution of the plug-in will fail.
@@ -85 +89 @@
 3. Installation
 
-v) Install the plug-in in the server file system.
+v) Install the plug-in in the BASE application server file system.
 
   make BASEDIR=<base-dir> install
@@ -91 +95 @@
 where <base-dir> is to be replaced by the path to BASE. The plug-in
 will install in the recommended directory
-<base-dir>/plugins/se/lu/thep/RMAExpress, i.e. if you prefer another
+<base-dir>/plugins/se/lu/thep/affymetrix, i.e. if you prefer another
 location you need to change the Makefile.
+
+For advanced users only: <base-dir> can really be any directory
+readable for the user running your tomcat server. This may be handy if
+you run several servers on one machine but only want one common
+directory hierarchy for the plug-ins. Or, if you update the BASE
+application frequently and in the process create new directories for
+the newer core.
+
+ Remember this location for configuration of BASE below.
 
 
 4. BASE configuration
 
-vi) Make BASE aware of the new plug-in ... to be written.
+vi) Make BASE aware of the new plug-in:
+
+ - Login to BASE with plug-in administrative privileges.
+ - Choose 'Administrate' -> 'Plugins' -> 'Definitions'.
+ - Click on 'New...'. This will open up the 'Create plugin' pop-up
+   window. Type "se.lu.thep.affymetrix.RMAExpress" in the 'Class'
+   field and "<base-dir>/plugins/se/lu/thep/affymetrix/RMAExpress.jar"
+   in the 'Path' field. Replace <base-dir> with whatever you used in
+   item 3.v) above.
+ - Locate 'RMAExpress plug-in' in the list of plug-in and click on
+   it. On the page that appears, click 'New Configuration ...' and a
+   'Create configuration' pop-up will appear. Type an appropriate name
+   in the 'Name' field and click on the 'Save and configure' button.
+ - There is only one configuration option to set in the 'Configure
+   plugin' pop-up, the name and location of the RMAExpressConsole
+   binary. Click on the required option 'RMAExpressConsole ...' and
+   type the full path to the RMAExpressConsole binary from item 1.ii)
+   above.
+
+5. That's it, now you need to BASE skills to actually make use of the
+   RMAExpress plug-in. Read the README file for some pointers on what
+   to do now.

trunk/se/lu/thep/affymetrix/Makefile

@@ -28 +28 @@
 JAR  = RMAExpress.jar
 
-BINDISTFILES = Changelog INSTALL Makefile README RMAExpress.jar
+BINDISTFILES = Changelog COPYING INSTALL Makefile README RMAExpress.jar
 VERSION = pre0.1
 PACKAGEFILE = base_rmaexpress_plugin-$(VERSION)

trunk/se/lu/thep/affymetrix/README

@@ -53 +53 @@
 
 
-What is required to use the RMAExpress for BASE plug-in?
+What is required to use the RMAExpress plug-in for BASE?
 
-1) You need to install the plug-in, see INSTALL for instruction on how
-   to preform installation of this plug-in.
+1) You need to install the plug-in and make BASE aware of the new
+   plugin, see INSTALL for instruction for installation
+   instructions.
 
 2) You need to import probe set information into BASE (reporter
-   information), i.e. import AffyChip_annot.csv into BASE.
+   information), i.e. import AffyChip_annot.csv into BASE. This is
+   only needed to do once, and optionally later if reporter
+   information should be updated. This must be performed by a user
+   with reporter administrative privilieges, an ordinary BASE user do
+   NOT have this privilege.
+
+   - First you need to create an plug-in configuration for the
+     'Reporter importer' plug-in. Locate the 'Reporter importer'
+     plug-in definition ('Administrate' -> 'Plugins' ->
+     'Definitions'). Click on it and choose 'New configuration ...',
+     name the configuration and choose 'Save and configure'.
+
+   - A 'Parser settings' dialog will appear. Set fields according to
+     this list:
+
+       Data header  : "Probe Set ID","GeneChip Array",.*
+       Data splitter: (?!"),(?=")
+       Remove quotes: true
+       Name         : \Probe Set ID\
+       Reporter ID  : \Probe Set ID\
+
+    Finalize by clicking 'Next'.
+
+   - Import the reporters by choosing 'View' -> 'Reporters' and the
+     clicking on 'Import...'. Click 'Next' without changing the 'auto
+     detect' settings. Supply the filename in the next dialog, click
+     'Next'. Start the import by clicking 'Next' in the parameter
+     dialog.
 
 3) You need to define the design of the AffyChip in BASE, i.e. import

trunk/se/lu/thep/affymetrix/RMAExpress.java

@@ -184 +184 @@
         Request.COMMAND_CONFIGURE_PLUGIN,
         "Configure plugin",
-        "The executable for RMAExpressConsole",
+        "Set the path to the RMAExpressConsole executable",
         parameters);
     }
@@ -422 +422 @@
     ("RMAExpress plug-in", "Computes gene expression summary values for " +
      "Affymetrix Genechip data using the Robust Multichip Average " +
-     "expression summary", "$Revision$ $Date$",
-     "2006 Jari Häkkinen, Department of Theoretical Physics, Lund University",
+     "expression summary", "$Revision$ $Date$","2006 Jari Häkkinen, " +
+     "Department of Theoretical Physics, Lund University",
      null, "base@thep.lu.se", "http://baseplugins.thep.lu.se" );
   private RequestInformation configureJob = null;
   private RequestInformation configurePlugin = null;
   private static PluginParameter<String> execPathParameter =
-    new PluginParameter<String>("execPath","RMAExpressConsole executables path",
+    new PluginParameter<String>("execPath","RMAExpressConsole executable",
                                 "The path to the executable",
                                 new StringParameterType(255, null, true));