Step 1: Download Xenium Ranger from the Download Center page. Select either the Gzip (tar.gz) or Xzip (tar.xz) tarball. The smaller file size of the Xzip tarball enables faster download.

Step 2: Unpack the selected Xenium Ranger file in any location. For this example code, the tarball is installed in a directory called /opt. The tar command unpacks Xenium Ranger, its dependencies, and the xeniumranger script into a new directory called xeniumranger-xeniumx.y (i.e., xeniumranger-xenium3.0).

• Unpack Gzip file:

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cd /opt
tar -xzvf xeniumranger-x.y.z.tar.gz

• Unpack Xzip file:

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cd /opt
tar -xvf xeniumranger-x.y.z.tar.xz

Step 3: Prepend the Xenium Ranger directory to your $PATH. This allows you to invoke the xeniumranger command. For convenience, you can add this command to your .bashrc or .bash_profile so the path is exported automatically after the file is sourced. Alternatively, if running Xenium Ranger in job submission mode, you can add this command to the job script so it runs each time you use the pipeline.

In this example, we export the path to Xenium Ranger v3.0:

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export PATH=/opt/xeniumranger-xenium3.0:$PATH

To ensure that the xeniumranger pipeline is installed correctly, run the help command:

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xeniumranger --help

The help output should look like this:

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Process 10x Genomics Xenium data

Usage: xeniumranger <COMMAND>

Commands:
  relabel              Correct the gene labels applied to decoded transcripts
  resegment            Resegment cells and or nuclei with adjusted segmentation parameters. All secondary results are recomputed
                       and a new output bundle is generated
  import-segmentation  Import a 3rd party segmentation and redo secondary analysis using the new segmentation
  upload               Upload analysis logs to 10x Genomics support
  sitecheck            Collect linux system configuration information
  help                 Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version