Windows

How to set up tb-profiler locally on a windows machine

Sadly the bioinfomatic software that tb-profiler depends on does not run on Windows, so it can't be installed with conda. There is another option though - to run with docker. This quick guide will run through how to set up docker and set it up to run tb-profiler.

Step 1 - Download and install docker

Go to https://docs.docker.com/desktop/windows/install/ to get the latest docker installation file. After it downloads, execute it and go through the recommended steps. During the installation process you might be asked to restart your computer a few times.

After it finishes it will prompt you to install WSL 2.

Again, follow the link on the prompt (https://aka.ms/wsl2kernal) and follow the instructions.

Install tb-profiler docker image

Each new release on conda is also built for docker and is available on quay.io. To get the image click the start menu and open up a program called PowerShell

Once this is open type in the following:

docker pull quay.io/biocontainers/tb-profiler:4.3.0--pypyh5e36f6f_0

Create a container

Now that you have the image you can set up a container. To do this you can open up Docker Desktop which was installed as part of the Docker installation. Navigate to the "Images" tab and the hover over the tb-profiler image and click "Run". Expand the "Optional settings" section and fill in the Volumnes box. This allows you to map a folder on your local machine to a directory in the linux container:

• Host path: click the three dots to help you select the folder

• Container path: type in "/mnt"

Then click "Run"

Open up a terminal from the container

Now navigate to the "Containers" tab in Docker Desktop, hover over the container and click on the "CLI" button as indicated below.

This will open up a terminal window where you can run linux commands - including tb-profiler!

First navigate to the "/mnt" directory and then run tb-profiler as shown elsewhere in this documentation.

cd /mnt
tb-profiler profile -h