FragPipe license

[rolivella]

Hello,

I have created a container using the software available in this repository, as per the Dockerfile provided here. I would like to redistribute this container image via DockerHub.

Could you please clarify if I am allowed to do so under the terms of the license associated with this project? Specifically, I would like to know if redistributing the Docker image I have built is compliant with the project's licensing terms, and if there are any additional steps or permissions I need to obtain before doing so.

Best regards

[anesvi]

You cannot include the tools that the user needs to download separately (MSFragger, IonQuant, diatracer) but the rest of FragPipe (what is included in the FragPipe zip folder) is fine to redistribute. Note that academic users can get MSFragger and IonQuant through bioconda, this is how Galaxy users can get them.

[rolivella]

Good, thanks @anesvi !

[fcyu]

I have already create an Docker image using the dockerfile: https://hub.docker.com/r/fcyucn/fragpipe. May I ask why do you want to distribute another one with the same content?

Thanks,

Fengchao

[rolivella]

Ah, ok, since it’s already available, I’ll go ahead and use that instead of creating my own. Thanks for making it available!

[rolivella]

@fcyu I made a small tutorial for running the container using Docker or Singularity that might be usefull for other users:

Running FragPipe with Docker and Singularity

This tutorial covers how to use Docker and Singularity to run FragPipe version 22.0. We will run the fcyucn/fragpipe:22.0 container, first with Docker, then converting it to a Singularity image.

Running FragPipe with Docker

1. Pull and run the Docker container:

   To run the FragPipe tool directly using Docker, execute:

   docker run fcyucn/fragpipe:22.0 fragPipe-22.0/fragpipe/bin/fragpipe --help

   This command will:

   • Pull the fcyucn/fragpipe:22.0 image from Docker Hub.
   • Run the fragpipe command inside the container, displaying the help options.

2. Save the Docker image to a TAR file:

   To convert the Docker container for use in Singularity, save the Docker image to a tarball:

   docker save -o fragPipe-22.0.tar fcyucn/fragpipe:22.0

   This command will export the Docker image into a file called fragPipe-22.0.tar.

Running FragPipe with Singularity

1. Convert the Docker image to a Singularity image:

   Use the exported Docker tarball to create a Singularity image:

   singularity build fragPipe-22.0.img docker-archive://fragPipe-22.0.tar

   This will convert the Docker image into a Singularity image named fragPipe-22.0.img.

2. Run the FragPipe tool with Singularity:

   Once the Singularity image is built, you can execute the fragpipe command with:

   singularity exec fragPipe-22.0.img /fragpipe_bin/FragPipe-22.0/fragpipe/bin/fragpipe --help

   This command runs the same fragpipe tool using the Singularity image, displaying the help options.

[fcyu]

I had one here https://fragpipe.nesvilab.org/docs/tutorial_docker.html. Maybe you can send a PR to merge yours with mine?

Thanks,

Fengchao

[rolivella]

I would like to but I couldn't find the tutorial_docker.html

[fcyu]

It's in the gh-pages branch: https://github.com/Nesvilab/FragPipe/blob/gh-pages/docs/tutorial_docker.md

Thanks,

Fengchao

[rolivella]

done: #1833