OST Docker

Build Docker image

In order to build OST image:

cd <PATH TO OST>/docker
docker build --tag <IMAGE NAME> -f Dockerfile .

or if you downloaded the Dockerfile directly:

docker build --tag <IMAGE NAME> -f <DOCKERFILE NAME> <PATH TO DOCKERFILE DIR>

You can chose any image name (tag) eg. ost. Here we only keep the recipe for the most recent version of OpenStructure. To build an image for a different version, you can either adapt the OPENSTRUCTURE_VERSION variable in the recipe or look in the git history for an older recipe.

Testing the image

One can find a exemplary script (test_docker.py) in the downloaded directory. To run it do:

cd <PATH TO OST>/docker
docker run --rm -v $(pwd):/home <IMAGE NAME> test_docker.py

As the last line you should see OST is working!.

Run script and action with OST

docker run --rm -v /home/user:/home <IMAGE NAME> script.py pdbs/struct.pdb

docker run --rm -v /home/user:/home <IMAGE NAME> /home/script.py /home/pdbs/struct.pdb

Actions

To see the list of available actions do:

docker run --rm <IMAGE NAME> -h

To run chosen action do:

docker run --rm <IMAGE NAME> <ACTION NAME>

Here is an example run of the compare-structures action:

docker run --rm -v $(pwd):/home <IMAGE NAME> compare-structures \
    --model model.pdb \
    --reference reference.pdb \
    --output output.json \
    --qs-score \
    --residue-number-alignment \
    --lddt \
    --structural-checks \
    --consistency-checks \
    --inclusion-radius 15.0 \
    --bond-tolerance 15.0 \
    --angle-tolerance 15.0 \
    --molck \
    --remove oxt hyd unk \
    --clean-element-column \
    --map-nonstandard-residues

In order to see all available options for this action run:

docker run --rm <IMAGE NAME> compare-structures -h

Scripts

In order to run OST script do:

docker run [DOCKER OPTIONS] --rm -v <PATH TO SCRIPT DIR>:/home <IMAGE NAME> /home/<SCRIPT NAME> [SCRIPT OPTIONS]

Run ost with utility command

One can also use provided utility bash script run_docker_ost to run basic scripts and actions:

<PATH TO OST>/docker/run_docker_ost <IMAGE_NAME> [<SCRIPT_PATH>] [SCRIPT OPTIONS]

One just needs to provide image name and optionally a script/action and its options. It is useful to link the command to the binary directory eg. in linux:

ln -s <PATH TO OST>/docker/run_docker_ost /usr/bin/run_docker_ost

In order to run an exemplary script (test_docker.py) do:

cd <PATH TO OST>/docker
./run_docker_ost <IMAGE NAME> test_docker.py

To see the help for compare-structures action run:

cd <PATH TO OST>/docker
./run_docker_ost <IMAGE NAME> compare-structures

Run GUI

In order to run GUI do (tested on linux machine):

xhost +local:docker
docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix --entrypoint dng <IMAGE NAME>

Running other commands

The default entrypoint of the Docker image is "ost" thus in order to run other available commands (or other commands in general) one need to override the entrypoint:

docker run --rm -ti --entrypoint <COMMAND> <IMAGE NAME> [COMMAND OPTIONS]

Eg. to run molck type:

docker run --rm -ti --entrypoint molck <IMAGE NAME> --help