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Gabriel Studer's avatar
SCHWED-5907 Fixes for updated OST Singularity image
Studer Gabriel authored 
The following issues were observed:
- warning about non-writable directory which was set as IPYTHONDIR env var
  Not very surprising, it's a directory that lives in container space...
- stale kernels
  I didn't investigate that one properly. It had something to do with bending
  around all Jupyter/IPython relevant directories to custom set directories
  in the image. Reason for doing that is potential Python modules that reside
  in user home of the host that get imported in the container. I removed the
  bending around with the full knowledge that the described problem may occur.
- version updates
  Some changes related to different Python versions between old base image
  (Ubuntu 20.04) and the new one (Ubuntu 22.04).
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Gabriel Studer's avatar 185fa65d
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README.rst
Singularity
README.rst

OST Singularity

Building Singularity image

In order to build OST Singularity image:

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

Note

Running singularity build command requires root permissions (sudo).

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, edit the source line (From:) 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 run-help --app <APP NAME> <PATH TO OST IMAGE>

Eg.:

singularity run-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.