Command-Line Interface
TruSight Software includes a command-line interface (CLI) that supports uploading FASTQ files and downloading analysis files.
Requirements
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The CLI tool requires JVM 8 and is intended to run on Linux CentOS. |
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The user associated with the API key must be a domain administrator and a member of the workgroup to which the files are uploaded. |
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Configuration files created in release 0.6 or earlier must be deleted from <HOME>/.illumina/. |
Set Up the Tool
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Select Download CLI Tool from the Account drop-down list. |
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Configure the tool using the configure command. Use a backslash character to escape any non-alphanumeric characters in the API Key. |
java -jar wgs-cli-<version>.jar --configFilePath <configfilepath> configure --domain <domain> --workgroup $<workgroupid> --url $<url> --apiKey <apiKey>
Where:
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version is the CLI version. |
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configfilepath is the path for the configuration file. If no path is specified, <HOME>/.illumina/uploader-config.json is used. |
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domain is the user domain (eg, wgs). Required. |
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workgroupid is the workgroup ID, which is available from the Workgroup Admin Console URL. Required. |
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url is the WGS URL, excluding http (eg, mycustomdomain.illumina.com). |
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apiKey is the API key provided by Illumina, modified with backslashes if necessary. |
NOTE
The API key can optionally be written directly to the uploader-config.json file after configuration.
The command creates a configuration file with the specified parameters and saves the file to
Example:
java -jar wgs-cli.jar --configFilePath cliConfig/customConfig.json configure --domain wgs --workgroup $12345-45667-234234 --url mycustomdomain.illumina.com --apiKey "abrt\(tCZD\@Kht0\#f8"
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[Optional] To make changes to the configuration, use the configure command or directly edit the file. Escape any non-alphanumeric characters with a backslash character. |
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Copy the URL into your browser, and then log on to your account. |