Tools included in the container are MGL Tools and AutoDock Vina. Two versions are available: nvidia and mesa-supported container. For nvidia support, you need to install NVIDIA driver on host and install nvidia-docker2.
To download:
- docker pull afandiadib/autodock:nvidia
- docker pull afandiadib/autodock:mesa
Example of usage:
To run autodock tools:
docker run --rm --user=$(id -u) \
--workdir=`pwd` \
--env=DISPLAY \
--volume=/home/$USER:/home/$USER \
--volume=/media:/media \
--volume=/mnt:/mnt \
--volume=/etc/group:/etc/group:ro \
--volume=/etc/passwd:/etc/passwd:ro \
--volume=/etc/shadow:/etc/shadow:ro \
--volume=/etc/sudoers.d:/etc/sudoers.d:ro \
--volume=/tmp/.X11-unix:/tmp/.X11-unix:rw \
--volume=/usr/share/icons:/usr/share/icons \
--device=/dev/dri \
afandiadib/autodock:nouveau adt
If permission denied, you need to change ownership of /dev/dri on host for gpu acceleration.
sudo chown -R $USER /dev/dri
To run autodock tools:
docker run --rm --user=$(id -u) \
--workdir=`pwd` \
--env=DISPLAY \
--volume=/home/$USER:/home/$USER \
--volume=/media:/media \
--volume=/mnt:/mnt \
--volume=/etc/group:/etc/group:ro \
--volume=/etc/passwd:/etc/passwd:ro \
--volume=/etc/shadow:/etc/shadow:ro \
--volume=/etc/sudoers.d:/etc/sudoers.d:ro \
--volume=/tmp/.X11-unix:/tmp/.X11-unix:rw \
--volume=/usr/share/icons:/usr/share/icons \
--runtime=nvidia \
afandiadib/autodock:nvidia adt
docker run --rm \
--workdir=`pwd` \
--volume=`pwd`:\`pwd\` \
afandiadib/autodock:nouveau vina
To run vina, alias the docker command in .bashrc for convenience:
alias vina='docker run --rm --workdir=`pwd` --volume=`pwd`:`pwd` afandiadib/autodock:nouveau vina'
For virtual screening, it is better to run interactively though.