Pulling and running FragPipe using Docker
- Install Docker
- 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/
- 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.