Lefse commands in docker

Downstream analysis and statistics LEfSe
1

Hello,
since the Galaxy lefse server is not working these days, I am trying to analyze it using the docker container. I’m new to this, where do I have to include the file I want to analyze?
Where are the created files saved?
Could someone give me a more detailed manual on using Lefse in Docker?

1 Like
2

Hello @CMR ,

Apologies for the delay.
To pull the “biobakery/lefse” Docker Hub image and run a container using that image, follow these steps:

  1. Install Docker: If you haven’t already, you need to install Docker on your system. You can download it from the official Docker website.
  2. Pull the “biobakery/lefse” Image:Open a terminal or command prompt and use the docker pull command to pull the “biobakery/lefse” image:
docker pull biobakery/lefse
  1. Run a Container from the “biobakery/lefse” Image:Now that you’ve pulled the image, you can run a container using it:
docker run --name my-lefse-container -d biobakery/lefse

This command creates a container with the name “my-lefse-container” and runs the “biobakery/lefse” image in the background.

  1. Access the Container:To access the container’s shell or execute commands within it, you can use the docker exec command. For this image, you might not have an interactive shell, but you can still execute commands inside the container:
docker exec -it my-lefse-container /bin/bash

This example uses /bin/bash as the command to execute within the container. Replace it with the appropriate command you want to run.

  1. Manage the Container:To stop or remove the container, you can use the following commands:
  • Stop the container: docker stop my-lefse-container
  • Remove the container: docker rm my-lefse-container

Note: You will be able to include the file you want to analyze after the docker exec step after you can login inside the created lefse docker container.

Regards,
Sagun

1 Like