Installation v0.0.0

Prerequisites

In order to run the PanVA application you will need the following:

• Docker
• A database that follows the PanVA API Data Format
• Optional: A frontend configuration file.

Running PanVA with Docker recommended

Using the publically available Docker image, you can start the PanVA application from anywhere using the following command:

docker run -p 8080:80 -v /path/to/your/data:/panva/api/data -v /path/to/your/config.json:/panva/frontend/config.json -e APACHE_UID=1000 -e APACHE_GID=1000 ghcr.io/panbrowse/panva:main

The application will then be available on http://localhost:8080/.

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Ensure Docker is running and has access to data directories before running the command.

We'll explain the various options passed to Docker:

option	explanation
-p 8080:80	The image exposes port 80. This option maps that port to port 8080 on the host machine.
-v /path/to/your/data: /panva/api/data	Mounts your custom data directory to the predefined path /panva/api/data that the application looks at. Note: Make sure this directory is writable so the linkage_matrix.npy files can be stored in each homology group directory.
(OPTIONAL) -v /path/to/your/config.json: /panva/frontend/config.json	Mounts your custom config.json file to the predefined path /panva/frontend/config.json that the application looks at. Note: The apiUrl option should be omitted in most cases.
(OPTIONAL) -e APACHE_UID=1000 -e APACHE_GID=1000	The data directory mounted at /panva/api/data needs to be read by the Apache webserver. To prevent permission issues, the user id (uid) and group id (gid) of the user running Apache can be changed to match the data directory on the host machine. Use ls -n to see the numeric uid and gid of a directory on the host machine.
(OPTIONAL) --name panva_instance	Sets a name for your container. If not specified, the container gets a random name that is visible in Docker Desktop.

Building the application

WARNING

For most use cases, building a custom docker image is not needed

To run the application, you don't need to build the application yourself. In most cases running the application via the public Docker image is what you're looking for.

You can, however, build a Docker image of the application yourself. From the root of this repository run the following command:

docker build -t panva .

When running the application, instead of using the provided Docker image name you use the panva tag instead:

docker run [options] panva

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More information for development can be found here