# Using the BaseSpace Command Line Interface (CLI) Tool on the NovaSeq X Series ### **Background** The BaseSpace CLI tool allows a user to upload run data to BaseSpace for monitoring run metrics or performing data analysis in the cloud. As the NovaSeq X Series instruments splits certain run data across two different locations, this requires the use of specific command line options to ensure the data is uploaded correctly. ### **Installing and Authorizing the CLI Tool** 1. Login to the instrument using the `ilmnadmin` Linux Operating System (OS) account. 1. If currently logged in as `ilmnuser`, exit the Control Software and log out of the `ilmnuser` account, then log into the Linux OS using the `ilmnadmin` account. 2. Open Chromium and navigate to the [BaseSpace CLI Overview](https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview) page, then download the **Linux CLI Tool** to the /home/ilmnadmin/Downloads directory on the instrument. 3. From the Linux OS, select the **Activities** menu in the top-left corner, then open the **Terminal** app. 4. Input the command cd \~/Downloads and press **Enter** to navigate to the **Downloads** directory. 5. Input the command `chmod 775 bs` and press **Enter** to enable script execution permissions for the CLI script. 6. Input the command ./bs auth to generate an authorization link. 7. Hold the **Ctrl** button and then click the link to open the link in **Chromium**, then input your BaseSpace login credentials. 8. On successful authentication, the **Terminal** will show a successful login message. **General CLI Syntax** The CLI Tool will use the following syntax for identifying the location of files to send to BaseSpace. Different options can be used to specify separate locations for the RunParameters.xml and SampleSheet.csv files, as well as directories to omit depending on the user needs. For each command, the \[ ] are placeholders and should be omitted from the final command after inputting the RunName, InstrumentType, and RunID information. ./bs upload run -n \[RunName] -t \[InstrumentType] \[OPTIONS] /usr/local/illumina/mnt/runs/\[RunID] * upload run Calls the 'upload run' module within the CLI Tool * -n \[RunName] Provides BaseSpace with a name for the sequencing run. * -t \[InstrumentType] Provides BaseSpace with the instrument type, either `NovaSeqX` or `NovaSeqXPlus`. * \[OPTIONS] Provides the CLI Tool with options including location of the RunParameters.xml or SampleSheet.csv files, as well as directories and files to skip if they are not needed. * /usr/local/illumina/mnt/runs/\[RunID] Provides the CLI Tool with the location of the run data on the instrument. ### **Uploading Run Metrics Files Only (Cloud Run Monitoring)** This command will trigger upload of the run metrics files only and is similar to the **Cloud Run Monitoring** option. The general syntax for the command is as follows: ./bs upload run -n \[RunName] -t \[InstrumentType] --run-parameters=/usr/local/illumina/runs/\[RunID]/RunParameters.xml --skip-dir=Data/ --skip-dir=Thumbnail\_Images/ --exclude='\*.out' /usr/local/illumina/mnt/runs/\[RunID] * \--run-parameters=/usr/local/illumina/runs/\[RunID]/RunParameters.xml Provides the CLI Tool with the specific location of the RunParameters.xml file. * \--skip-dir=Data/ --skip-dir=Thumbnail\_Images/ Forces the CLI Tool to skip the Data/ and Thumbnail\_Images/ directories as these are not needed for Cloud Run Monitoring. * \--exclude='\*.out' Indicates to the CLI Tool to skip certain log files that are not required for upload to BaseSpace. **Uploading Run Metrics and Data Files for Analysis (Cloud Run Storage)** This command will trigger upload of both run metrics and run data files to BaseSpace and is similar to the **Cloud Run Storage** option. This method will be required if the user intends to use Cloud Apps such as such as BCL Convert or other DRAGEN Apps to process the data in the Cloud. If a SampleSheet.csv file is available, it can be uploaded and will automatically trigger analysis with the configured Apps listed in the SampleSheet.csv file. If a SampleSheet.csv file is not available at the time of upload, this option can be omitted from the command entry. ./bs upload run -n \[RunName] -t \[InstrumentType] --run-parameters=/usr/local/illumina/runs/\[RunID]/RunParameters.xml --samplesheet=/usr/local/illumina/runs/\[RunID]/SampleSheet.csv --skip-dir=Thumbnail\_Images/ --exclude='\*.out' /usr/local/illumina/mnt/runs/\[RunID] * \--run-parameters=/usr/local/illumina/runs/\[RunID]/RunParameters.xml Provides the CLI Tool with the specific location of the RunParameters.xml file. * \--samplesheet=/usr/local/illumina/runs/\[RunID]/SampleSheet.csv Provides the CLI Tool with the specific location of the SampleSheet.csv file. * \--skip-dir=Thumbnail\_Images/ Forces the CLI Tool to skip the Thumbnail\_Images/ directory as this are not needed for Cloud Storage. * \--exclude='\*.out' Indicates to the CLI Tool to skip certain log files that are not required for upload to BaseSpace. \ \ \
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