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Step-By-Step Guide to Install and Use caArray Importer
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caArray Importer v1.0.2 can be downloaded from this page.
caArray Importer Compatibility
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Components | Description |
|---|---|
Java 2 Platform Standard Edition 5.0 Update 10 (J2SE 5.0) | Building and running Java applications |
Apache Ant 1.7.0 | Building and running Java applications |
Set JAVA_HOME and ANT_HOME environment variables | Refer to the caArray installation guide for further details |
caArray legacy client distribution | Download from the caArray GForge sitefiles archive (login required) |
Initial Configuration
The initial configuration of caArray Importer is specified by multiple parameters in the build.properties file, which is located in the root level of the caArray Importer distribution archive. For the parameters below, in most cases a user only needs to update the server.base.dir property. Note that the value for this property varies depending on the particular version of caArray you are running.
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Parameters | Description | ||
|---|---|---|---|
| The location of the caArray Java client distribution zip file. By default it is assumed to be in the current working directory and named caarray-client-legacy.zip. | ||
| The base directory in which the caArray server was installed. The directory provided depends on the exact caArray version you are running. | ||
| The actual deployment directory. Normally this does not need to be changed. This can be left empty if you do not have write access to the deployment directory. In that case, you must manually copy it over after the caarray.ear file is updated. | ||
| The target caarray server ear file. Normally this does not need to be changed. |
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An example client-side program is provided to demonstrate the creation of a new project and the upload, validation and import of array data files. The source code can be found in the following file:
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example/src/main/java/org/cruk/cri/caarray/client/CaArrayImporterExample.java
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- Make sure that your Java classpath includes the updated client library. (This is taken care of if you run the example using Ant as shown below).
- Upload the array design files for the Affymetrix Mapping 250K Nsp and Sty chips into caArray using caArray web interface.
- Create a directory called arraydata in the same location as that in which you execute the client-side program.
- Copy a few Affymetrix 250K data files (CEL, CHP) and optionally MAGE-TAB IDF and SDRF files to the arraydata directory .
Run command below:
Code Block $ ant compile-example $ ant run-example
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- Upload the related array designs into the caArray web interface.
Modify the values for the following constants in
CaArrayImporterExample.java. Note that the values provided are for illustration purpose only and must be replaced:Code Block private static final String SERVER_HOST = "yourCaArrayServerHost"; private static final int SERVER_JNDI_PORT = 31099; private static final String USERNAME = "yourUsername"; private static final String PASSWORD = "yourPswd"; public static String TITLE = "Test Affymetrix Expression Project"; public static String PROVIDER = "Affymetrix"; public static String ASSAY_TYPE = "Gene Expression"; public static String[) ARRAY_DESIGNS = new String(] \{ "HG-U133_Plus_2" \};If you have your data files stored under a directory (for example:
C:/data/caarray/MAGEdataFiles) different from the arraydata created in scenario 1, replace the directory arraydatawith the path to that directory as shown below in the function "main". It can be either relative or absolute path:Code Block client.uploadFiles(project, "C:/data/caarray/MAGEdataFiles");- Copy a few Affymetrix HG-U133_Plus_2 data files (CEL, CHP) and optionally MAGE-TAB IDF and SDRF files to the C:/data/caarray/MAGEdataFiles directory .
Run the command below:
Code Block $ ant compile-example $ ant run-example
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Please leave your comments in caArray End User Forum
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