Using a Custom DIA-NN Version

This workflow includes DIA-NN version 1.8.1, which is the latest version that may be hosted in a public cloud container registry due to licensing restrictions. However, newer versions of DIA-NN can be used by building a Docker image on the system where you will run the workflow.

A build script is provided that automates this process. It downloads the necessary files from this project’s GitHub repository and builds the Docker image for you.

Note

These instructions only support DIA-NN version 2.x releases.

Important

All commands on this page are typed in the command line (also called a terminal). If you are on Windows, this means the Ubuntu terminal in WSL2. See How to Install the Workflow for how to open a command line on your system.

Prerequisites

Before you begin, ensure the following are installed and working on your system:

  • Docker: Required for building and running container images.

  • Nextflow: Required for running the workflow.

  • wget: Used by the build script to download files. Usually pre-installed on Linux.

If you have not yet installed these, see How to Install the Workflow for instructions.

You can verify Docker is working by running:

docker run hello-world

If you see a “Hello from Docker!” message, Docker is working correctly.

Step 1: Download the Build Script

wget https://raw.githubusercontent.com/mriffle/nf-carafe-ai-ms/main/resources/diann-docker/build_diann_docker.sh

Step 2: Run the Build Script

Run the script with the DIA-NN version number you want to use. You can find available versions at https://github.com/vdemichev/DiaNN/releases.

For example, to build DIA-NN version 2.3.2:

bash build_diann_docker.sh 2.3.2

The script will download the necessary files, build the Docker image, and print instructions when it is finished. This may take a few minutes.

Note

If you see an error that the Docker image already exists, you have already built this version. If you want to rebuild it, run the command shown in the error message to remove the existing image first.

To see all available options, run:

bash build_diann_docker.sh -h

Step 3: Configure the Workflow

After the script completes, it will display the exact line to add to your pipeline.config file. Open your pipeline.config (see How to Run the Workflow for how to find and edit this file) and add the line to the params section. For example, if you built version 2.3.2:

params {
    images.diann = 'diann:2.3.2'

    // ... your other parameters ...
}

After saving your pipeline.config, run the workflow as you normally would (see How to Run the Workflow). The workflow will automatically use your custom DIA-NN version for the DIA-NN search step.

Verifying the Version

After the workflow completes, you can confirm which version of DIA-NN was used by checking the versions.txt file in the results directory. See Output & Results for more information about output files.