README.rst

OST Singularity

Note

In order to run some singularity commands there might be a need to run them as root (sudo).

Build Singularity image

In order to build OST Singularity image:

cd <OST ROOT>/singularity
singularity build ost.img Singularity.1.7.1

One can chose any name for an image. For the purose of this file we will assume that the image name is ost.img.

Available apps

OST

The OST app exposes OpenStructure binary and can be used to run interactive shell and scripts.

To invoke OST shell run:

In order to run OST script do:

Warning

If script requires some external files eg. PDBs, they have to be located in the path accessible via mounted volumes. By default Singularity mounts $HOME and goes to CWD. Thus this sould work as expected out of the box.

One can find a exemplary script (test_docker.py) in the <OST ROOT>/docker directory. To run it do:

cd <OST ROOT>/singularity
singularity run --app OST ost.img ../docker/test_docker.py

lDDT

This app runs the Local Distance Test. To see more details run:

cd <OST ROOT>/singularity
singularity run --app lDDT ost.img

Molck

This app runs the Local Distance Test. To see more details run:

cd <OST ROOT>/singularity
singularity run --app Molck ost.img

Notebook

Probably the best way to play with OpenStructure is to run it wihtin the Jupyter notebook. In order to so run:

cd <OST ROOT>/singularity
singularity run --app Notebook ost.img

Copy the URL to the browser and launch the notebook with OST kernel. This will load all necessary OST components just like in the OST shell. We also enabled the nglview widget to interactively view molecular structures and trajectories. For more details on how to use nglview see the documentation.

Warning

As the Singularity mounts $HOME by default Jupyter and Ipython config files are moved to separate directories. Proper environmental variables are also set. In addition, Jupyter is run in a separate virtualenv to not interact with possibly installed host version.