Open terminal and pull the Docker image: docker pull fcyucn/fragpipe
(optional) Check the pulled image: docker image ls -a
Create a Docker container: docker run -it -v <host directory>:<container directory> fcyucn/fragpipe /bin/bash. <host directory> is the directory in your host machine, and <container directory> is the directory you want to map the host directory to container.
Then, you have entered the Docker container, and FragPipe is located in /fragpipe_bin
Go to /fragpipe_bin/fragpipe-x.x/fragpipe-x.x/bin directory and execute ./fragpipe --help in the terminal
Pulling and running FragPipe using Singularity
Install Singularity
Open terminal and pull the Docker image: singularity pull docker://fcyucn/fragpipe:latest
Enter the image: singularity shell --compat --bind /storage:/storage fragpipe_latest.sif /bin/bash
Then, you have entered the Singularity image, and FragPipe is located in /fragpipe_bin
Go to /fragpipe_bin/fragpipe-x.x/fragpipe-x.x/bin directory and execute ./fragpipe --help in the terminal
If you are using Apptainer, just replace singularity with apptainer in the commands.