Technical test v0.0.0

We strongly recommend to start with this technical test of the installation on a small yeast dataset before running PanVA on your own data.

From raw data to PanVA instance

PanVA requires data that follows this format.

PanTools and PanUtils

We recommend to use our PanUtils pipelines to go generate input data in the correct format. Three PanUtils pipelines can be used in the following order:

1. QC: Filter and do quality control of raw data
2. Pantools functions: Build a pangenome and run necessary analysis functions
3. Preprocessing PanVA: Preprocess the PanTools data must for PanVA.

INFO

The protocol with detailed steps for each pipeline is given here.

After running the pipelines and downloading the preprocessed data, you can continue to the PanVA protocol below.

PanVA

With the preprocessed data, we can launch a PanVA yeast instance in three simple steps. Before doing so, check whether your preprocessed data has the following directory structure with at least config.json, homologies.json, and genome_gene_distance.txt:

pangenome_db_grouping_v1_panva_input/
   └─ homology/
       ├─ config.json
       ├─ homologies.json
       ├─ genome_gene_distance.txt
       └─ [<homology_id> directories]

1. Install and run Docker. With Docker Desktop, make sure the application is running. To check whether Docker is succesfully installed, open the terminal and run:

docker --version

2. Run PanVA. From any location, run this command in your terminal, changing the two parameter paths explained below to your own setup:

docker run -p 8080:80 --name panva_yeast -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

• /path/to/your/data

  path should point to a directory containing a /homology directory, e.g.,: {YOUR_FULL_PATH}/pangenome_db_grouping_v1_panva_input
  Note: Make sure this data directory is writable

• /path/to/your/config.json

  provide the full path to the PanVA config file. This file can be found in the root folder of the exported data, e.g.,: {YOUR_FULL_PATH}/pangenome_db_grouping_v1_panva_input/homology/config.json

More information about the (optional) parameters can be found on the Installation page.

3. That’s it! 🎉 You can now view your browser instance at: http://localhost:8080.