Software Installation¶

Anaconda on Cheaha¶

For additional general information on using Anaconda please see Anaconda Environments.

If you are using Jupyter Notebook, please see our section on Packages for Jupyter.

Loading Anaconda¶

Anaconda is installed on Cheaha as a family of modules, and does not need to be installed by Researchers. Instead, the most recent version of Anaconda installed on Cheaha may be loaded using the command module load Anaconda3. Other versions may be discovered using the command module avail Anaconda. We recommend always using the latest version.

Note

If you are using Open OnDemand Jupyter Notebook you do not need to use the module load command as part of creating the job.

Using Anaconda¶

Anaconda on Cheaha works like it does on any other system, once the module has been loaded, with a couple of important differences in the callouts below.

Note

The base environment is installed in a shared location and cannot be modified by researchers. Other environments are installed in your home directory by default.

Important

Only create environments on compute nodes. Anaconda environment creation consumes substantial resources and should not be run on the login node.

Warning

The Cheaha operating system has a version of Python installed. This version is used by python calls when Anaconda has not been loaded. This can cause unexpected errors. Be sure you've loaded the Anaconda environment you need before using Python.

Danger

Do not use conda init on Cheaha! Anaconda is managed as a module, including script setup. Using conda init at any point can cause hard-to-diagnose issues with Open OnDemand Interactive Jobs. Please see this ask.ci FAQ for how to undo what conda init does.

If the Anaconda software instructs you to use conda init while on Cheaha, please ignore it to avoid future issues with Open OnDemand.

For more information on usage with examples, see Anaconda Environments. Need some hands-on experience, you can find instructions on how to install PyTorch and TensorFlow using Anaconda in this tutorial.

Obtaining the Latest CUDA and cuDNN Modules¶

Please see our CUDA and cuDNN section of the GPU page.

Cell Ranger¶

Cell Ranger is a proprietary software developed by 10x Genomics.

Licensing¶

(i) Usage of Cell Ranger is governed by the terms of their End User License Agreement (EULA).

(ii) Cell Ranger is strictly licensed for use with data generated on 10x Genomics instruments and may not be used with data from other platforms.

Installation¶

Cell Ranger can be installed within a researcher’s individual user account on Cheaha. Installation instructions are available on the official 10x Genomics website. You will have to use a compute node in Cheaha to install and run the software. For more information refer to Login Vs Compute Nodes.

Following are steps to install Cell Ranger in Cheaha, based on the instructions provided in the official site, linked above, as of 2025-06-01. Actual instruction steps may change over time.

Register and download the desired version of Cell Ranger from the 10X Genomics site.
Once registration is complete, you will be redirected to the download page with installation instructions. To begin, use the curl or wget command to download the .tar.gz package.
Next, extract the Cell Ranger package using the command below. In this example, version 9.0.1 is used:
```
$tar -zxvf cellranger-9.0.1.tar.gz
```
After the extraction is complete, navigate to the cellranger directory’s bin folder and print its path using the pwd command, as shown below:
```
$cd cellranger-9.0.1/bin
$pwd
```
The pwd command will display the full path to the bin directory. For example: /home/$USER/cellranger-9.0.1/bin

Note

The actual path may vary depending on where the folder is located in your account.
To add the above path to your .bashrc file, run the following command,
```
$echo "export PATH=\$PATH:/home/$USER/cellranger-9.0.1/bin" >> $HOME/.bashrc
```
This will append the export line to the end of your .bashrc file. You should see an entry similar to the following:
```
$export PATH=$PATH:/home/$USER/cellranger-9.0.1/bin
```
You can verify the addition by running:
```
$cat $HOME/.bashrc
```
To apply the changes, either close the terminal and open a new one, or run the following command:
```
$source ~/.bashrc
```
Then, verify that Cell Ranger 9.0.1 is correctly installed by running:
```
$cellranger --version.
```
You should see an output like:
```
$cellranger cellranger-9.0.1
```

Singularity Containers¶

Containers are a very useful resource for installing software without needing administrator permission. Please read the full documentation about singularity and containers on our main Singularity page.