OST Singularity

Building Singularity image

In order to build OST Singularity image:

cd <OST ROOT>/singularity
sudo singularity build ost.img Singularity.1.8.0

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

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.

Available apps

This container includes the following apps:

• OST - OpenStructure binary
• IPython - OST-powered iPython shell
• Notebook - A Jupyter notebook playground with OST and nglview
• lDDT - The Local Distance Difference Test
• Molck - Molecular checker
• ChemdictTool - Creating or update a compound library

To see the help for each individual app run:

singularity help --app <APP NAME> <PATH TO OST IMAGE>

Eg.:

singularity help --app OST ost.img

Facilitating the usage

For each of these apps it is useful to create an alias if they will be frequently used. Eg. to create an alias for IPython app one can run:

alias ost_ipython="singularity run --app IPython <PATH TO OST IMAGE>"

Then (in the same terminal window) to invoke IPython app one can just type:

ost_ipython

To make the alias permanent put it into your .bashrc file or whatever file you use to store the aliases.