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Installing Software in OpenScienceLab

• pip
  • Install pip package inside conda environment
• mamba
  • Install conda packages within a running notebook
  • Install conda packages from the terminal
• apt and apt-get

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pip

What is pip?

pip is a package installer for Python.

You can install pip packages onto your account in the following manner:

NB: Your installed pip packages are in the /home/jovyan/.local/lib/python3.x/site-packages directory.

1. Open a terminal and use the following command:

python -m pip install --user <package_name>

Install pip package inside of a conda environment

1. Open a terminal and use the following commands:

conda activate <environment_name>
python -m pip install --user <package_name>

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mamba

Users can install additional software with mamba in OpenScienceLab.

NB: OpenScienceLab began using mamba instead of conda to install conda packages in 2022. Since the syntax for mamba is identical to conda syntax, users who used conda previously should be familiar with the mamba workflow. Nonetheless, it is still worthwhile to reference conda documentation due to its similarity.

Packages installed in the base conda environment will not stay after the server shuts down. You will need to reinstall it during subsequent OpenScienceLab sessions. However, changes to non-base will persist. Therefore, we recommend installing new packages in your non-base environments rather than in the base.

Install conda packages within a running notebook

1. Edit a notebook code cell
   • Then use the following command: %mamba install <package_name>
2. Run the code cell

Install conda packages from the terminal

1. Open a terminal and use following command:

mamba activate <environment_name>
mamba install <package_name>

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apt and apt-get

At this time, users cannot install software in OpenScienceLab using apt or apt-get.