source: trunk/uk/ac/ebi/AffyArrayDesignBatchImporter/README.txt @ 456

Last change on this file since 456 was 441, checked in by dominic, 15 years ago

added changed the ebi-utils- apis, readme.txt,changelog and dependent jars

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1Release Note of Affymetrix Array Design Batch Importer
2============================================================
3General Information:
4---------------------
5
6This plugin imports array designs for affymetrix - single channel- array design only. The entry point for this plugin in base 2 is the Array Design list page. Array LIMS->Array Designs. The array designs must be provided in a zip archive. The plugins will do the unpacking, creates the array designs using the array design file name and also attach the cdf, clf or bpmap file to the newly created array design. If an array design already exists, the plug-in skips the cdf, bpmap or clf file. Please note that only a user with an administrator role may execute this plugin.
7
8========================================================================================================
9
10To Install the plugin:
11----------------------
12  - Place AffyArrayDesignBatchImporter.jar into the $BASE2_HOME/www/plugins/ directory on your BASE2 server.
13  - Place ebi-plugins-utils.jar in your base installation class path : $BASE2_HOME/web-inf/lib
14  - Install as new plugins uk.ac.ebi.nugo.plugins.AffyArrayDesignBatchImporter.jar contained in  $BASE_HOME/www/plugins/AffyArrayDesignBatchImporter.jar  .
15 
16  1. Log in to BASE with plug-in administrative privileges,
17  2. In the BASE web client, go to Administrate->Plugins->Definition
18  3. Click New to define the plugin.
19  4. Set the class and path parameters, in the dialog that opens
20    Class: uk.ac.ebi.nugo.plugins.AffyArrayDesignBatchImporter.jar
21    Path: enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/AffyArrayDesignBatchImporter.jar
22  5. Click Save
23  The new plugins appears under the name "Affymetrix Array Design Batch Importer" in the plugins list and is now ready for use.
24
25  General Installation instruction is available at: 
26http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation
27
28===============================================================================================
29To use the plugin:
30--------------------
31  - Support only files in cdf, clf or bpmap format for affymetrix platform only.
32  - Upload the zip file into base2 without unpacking. The plugins will do the unpacking  for you.
33  - If  an array design already exists, the plug-in skips the cdf, bpmap or clf file.
34  - Please note that only a user with an administrator role may execute this plugin.
35
36  1. Go to Array Design, on the list page, Select the import tab.
37  2. On the screen that appears, select the AffyArrayDesignBatchImporter from the drop down list, leave the file format as auto-detect  and clicl Next
38  3. Select the zip file containing the array designs to import using the browse button. Click Next
39  4. On the next screen, click Next as the file configuration has been done for you.
40  5. On the next screen click Finish and wait for the job to complete. You will be shown the progress of the import in the dialog, with the page refreshing itself regularly.
41 
42Presto!! The plugin then unzips the files , create all the array design and also attach the cdf, clf or bpmap file to the newly created array design. Do refresh the Array Design page to see the newly created array designs.
43
44====================================================================================================
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