Space Ranger

Spaceranger is a set of analysis pipelines that process Visium Spatial Gene Expression data with brightfield and fluorescence microscope images. Spaceranger Manual

Installation

The spaceranger comes as a binary that doesnot require compiling. Use Firefox in Thinlic to download the software. You may create a folder called 'software' in your home or project directory and extract it to that location. Change pi-cnetid with the the group name. if using for personal purpose, you can use scratch storage available at $SCRATCH/$USER folder. Change the extraction location to /project/pi-cnetid/software, or somewhere else and use the following command:

tar -xzvf spaceranger-3.0.0.tar.gz --directory /project/pi-cnetid/software

Updating PATH

After extracting the software, update the PATH as follows:

Update PATH:

export PATH=/project/pi-cnetid/software/spaceranger-3.0.0:$PATH

Save in .bashrc: Command above will change the $PATH temperorly only for that bash shell. You can permanently update the PATH by appending the following command to the .bashrc file:

echo 'export PATH=/project/pi-cnetid/software/spaceranger-3.0.0:$PATH' >> ~/.bashrc

These commands will ensure that spaceranger-3.0.0 is extracted to the specified location and added to the PATH for permanent access as discussed here

Docker image can be executed using Apptainer.

• Tutorials

• Job Submission Mode

• Space Ranger Cluster Mode