Changeset 1166 for plugins/base2

Timestamp:

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

Author:

Jari Häkkinen

Message:

Fixes #235 and spelling.

Location:

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

Files:

• INSTALL (modified) (3 diffs)
• README (modified) (10 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.

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

@@ -1 +1 @@
 ----------------------------------------------------------------------
 {{{
-Copyright (C) 2008
+Copyright (C) 2008 Nicklas Nordborg
+Copyright (C) 2009 Jari Häkkinen, Nicklas Nordborg, Martin Svensson
 
 This file is part of Illumina plug-in package for BASE.
@@ -47 +48 @@
 The Illumina BeadArray Reader is a scanner that can read arrays including Illumina 
 Sentrix BeadChips and Sentrix Array Matrices (SAMs). Operation of the BeadArray 
-Reader and image aquisition from Sentrix arrays is handled by the Illumina BeadScan 
+Reader and image acquisition from Sentrix arrays is handled by the Illumina BeadScan 
 software.
 
@@ -85 +86 @@
 The column content in an IBS file is described below.
  - ''' Illumicode ''': A code corresponding to the Array_Address_Id in the 
- Illumina Sentrix Array binary manifest (BGX) file. Note that the Illuminacode 
+ Illumina Sentrix Array binary manifest (BGX) file. Note that the Illumicode 
  is a string (or integer) of varying length. The Array_Address_Id is a string with 
- a fixed lenght of 10 characters that consists of an Illuminacode padded with zeros.
+ a fixed length of 10 characters that consists of an Illumicode padded with zeros.
  - ''' N ''': The total number of beads used to calculate Mean GRN and Dev GRN.
  - ''' Mean GRN ''': The mean intensity.
  - ''' Dev GRN ''': Standard deviation of the mean intensity. 
 
-IBS files may contain some rows with Illumicodes that are not represented in the 
+IBS files may contain some rows with Illumicode that are not represented in the 
 BGX files. 
 Our interpretation is that some probes that used to be annotated with a gene has 
 later been considered poor by Illumina (as we have only observed an increase 
-in the number of unmatched probes for later bgx revisions). To avoid that the 
+in the number of unmatched probes for later BGX revisions). To avoid that the 
 raw data importer fails cause of some probes, listed in the IBS-file, couldn't 
 be found in BASE - you have to set plug-in parameter 'Probe not found=skip', 
@@ -116 +117 @@
 BGX files are tab separated text files composed of 3 sections named Heading, 
 Probes, and Controls respectively. The first section is the Heading section. 
-It is preceeded by a row containing the text [Heading]. In the Heading section 
+It is preceded by a row containing the text [Heading]. In the Heading section 
 some information is presented including the number of Probes and Controls 
 described in the BGX file. See below for an example of the Heading section.
@@ -127 +128 @@
 Number of Controls  1426
 }}}
-Following the Heading section is the Probes section wich is preceeded by a row 
+Following the Heading section is the Probes section which is preceded by a row 
 containing the text [Probes]. The first row of the Probes section, i.e., the row 
 after [Probes] contain the header for the Probes section. Following the Probes 
-section is the Controls section wich is preceeded by a row containing the text 
+section is the Controls section which is preceded by a row containing the text 
 [Controls]. The first row of the Controls section, i.e., the row after [Controls] 
 contain the header for the Controls section. Note that the header row for the 
@@ -194 +195 @@
 == Getting started ==
 
- 1. Install this package as described by the instructions in the INSTALL file.
- 2. Import reporter annotations. You will need one or more BGX files for this. 
+ 1. Install this package as described by the instructions in the
+    INSTALL file.
+ 2. 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.
+ 3. Import reporter annotations. You will need one or more BGX files for this. 
     BGX files can be downloaded from http://www.switchtoi.com/annotationfiles.ilmn.
      * Upload the BGX file(s) to BASE.
@@ -204 +215 @@
      * Finish the job registration and wait for the plug-in to complete.
      * Repeat this one time for each BGX file.
- 3. Create array designs. You will need one array design for each BGX file.
+ 4. Create array designs. You will need one array design for each BGX file.
      * Go to the Array LIMS -> Array designs menu.
      * Click on the New button.
@@ -218 +229 @@
      * Finish the job registration and wait for the plug-in to complete.
      * Repeat this for each BGX file.
- 4. Import raw data. You will need one or two IBS files.
+ 5. Import raw data. You will need one or two IBS files.
      * Upload the IBS file(s) to BASE.
      * Go to the View -> Raw bioassays menu.
@@ -232 +243 @@
      * Finish the job registration and wait for the plug-in to complete.
      * Repeat this for each set of raw data files.
- 5. Add your raw data sets to an experiment.
+ 6. Add your raw data sets to an experiment.
  
 Tip! Steps 1-3 only needs to be done a single time for a BASE installation. If more than
@@ -239 +250 @@
 
 Tip! The data import step in (4) above can be done for an entire experiment at a time.
-
-