Changeset 1166 for plugins/base2/net.sf.basedb.illumina/trunk/INSTALL

Timestamp:

Sep 28, 2009, 1:31:50 PM (14 years ago)

Author:

Jari Häkkinen

Message:

Fixes #235 and spelling.

File:

• plugins/base2/net.sf.basedb.illumina/trunk/INSTALL (modified) (3 diffs)

plugins/base2/net.sf.basedb.illumina/trunk/INSTALL

@@ -1 +1 @@
 ----------------------------------------------------------------------
 {{{
-Copyright (C) 2008
+Copyright (C) 2008 Jari Häkkinen, Nicklas Nordborg
+Copyright (C) 2009 Jari Häkkinen, Martin Svensson
 
 This file is part of Illumina plug-in package for BASE.
@@ -68 +69 @@
  15. Done. The Illumina plug-ins are now installed. You can now restart any job
     agents as well.
+ 16. Optionally, if not already done, disable use of the 'Illumina'
+    raw data type provided by a standard BASE installation; Simply
+    remove, or comment out, the `<raw-data-type>` entry for
+    `id='illumina'` in configuration file
+    `/path/to/base/WEB-INF/classes/raw-data-types.xml` and restart the
+    BASE server. If a user already used the 'Illumina' raw data type,
+    BASE will display an error message in the GUI. Either restore the
+    use of 'Illumina' raw data type or remove the data using
+    'Illumina' raw data type.
     
 Make sure that the job agents have access to the illumina-plugins.jar file, 
@@ -80 +90 @@
 already installed Illumina package.
  1. Do the step 1-3 as described in the installation instructions.
- 2. Then proceed with step 4. '''Caution:''' ''Any changes in the files on the local server must be transfered 
+ 2. Then proceed with step 4. '''Caution:''' ''Any changes in the files on the local server must be transferred 
   to the new configuration-files before they are copied.'' Copying the new files will overwrite the existing files.
  3. Do step 5-6 as described.
- 4. Step 7-9 are optional and only needed if the new release contains plugins or changed/new pluginconfigurations
+ 4. Step 7-9 are optional and only needed if the new release contains plugins or changed/new plugin configurations
     that you want to install. [[BR]]
     '''Notice1:''' Already installed plugins do not need to be re-installed(unless the jar-path has been changed), but updated configurations do.[[BR]]
     '''Notice2:''' If the existing configuration is not first removed  you will end up with two configurations with the same name. 
-    '''Notice3:''' Upgrading from 1.3.x or less require you to run the installation wizzard even for the installed plugins to update their jar-path.
+    '''Notice3:''' Upgrading from 1.3.x or less require you to run the installation wizard even for the installed plugins to update their jar-path.
  5. Step 10-13 are also optional and only necessary when the release comes with new Illumina variants that you want to create.
  6. Do step 14 to update the extensions.