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Xenium Ranger is a single, self-contained tar file that can be unpacked anywhere on your system. It bundles all of its required software dependencies, which are pre-compiled to run on a wide range of Linux distributions.

Please replace x.y.z with the Xenium Ranger version you wish to install.

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-xenium2.0).

  • Unpack Gzip file:
cd /opt tar -xzvf xeniumranger-x.y.z.tar.gz
  • Unpack Xzip file:
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 v2.0:

export PATH=/opt/xeniumranger-xenium2.0:$PATH

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

xeniumranger --help

The help output should look like this:

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