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Software environment

NaaVRE virtual labs provide a pre-configured software environment that powers:

  • Jupyter notebook kernels (for interactive coding).
  • Workflow components (when notebook cells are containerized).

Package Management​

The environment uses:

  • Conda Forge as the primary package manager. Conda Forge provides pre-built, compatible packages, ensuring reproducibility across platforms.
  • Dockerfiles for system libraries and packages not available in Conda Forge. Some low-level or system-specific dependencies require direct installation via Docker.

Inspecting the existing Conda environment​

To list the conda environment, do the following in a virtual lab:

Open a terminal through the Launcher.

Set conda as a source:

source /opt/conda/etc/profile.d/conda.sh

Find the name of the conda environment:

conda info --envs

# conda environments:
#
base                 * /opt/conda
vanilla                /opt/conda/envs/vanilla

In the example above the name is "vanilla".

Activate the conda environment:

conda activate vanilla

As a result, you should see the name of the environment at the start of the line:

(vanilla) jovyan@jupyter-lab-[lab- and username, current path]$

List the packages in the conda environment:

(vanilla) jovyan@jupyter-lab-[lab- and username, current path]$ conda export --from-history
name: vanilla
channels:
  - conda-forge
dependencies:
  - r-jsonlite=1.9.1
  - r-optparse=1.7.5
  - ipykernel=6.29.5
 ...

Including "--from-history" lists explicitly installed packages. Removing "--from-history" lists all installed packages including dependencies.

Updating the environment​

You can temporarily install packages yourself, or ask the NaaVRE DevOps team to permanently update your software environment in case you have your own virtual lab.

Temporary installation​

To install missing packages for the current virtual lab session only, use the following commands:

Python (pip)​

!pip install scipy

R (install.packages)​

install.packages("pracma")
note

Packages installed this way will not persist after your virtual lab session ends.

Permanent installation​

To install packages permanently, we need to update the software environment of your virtual lab. This requires that you own a virtual lab.

Step 1: Request you own virtual lab​

To become a virtual lab owner, propose your own virtual lab:

Propose your own virtual lab

Step 2: Installation Methods​

NaaVRE uses Conda Forge to manage environments. Creation and updating of environments is done by the virtual lab coordinator. Depending on the package, we will use one of the following methods:

  • Conda: Preferred for most packages.
  • CRAN/GitHub: Used for packages not available in Conda.
  • Dockerfiles: Required for system libraries or packages that cannot be installed via the above methods.

You can help speed up the process by providing Conda environment files (e.g., environment.yml) and links to CRAN packages or GitHub repositories.