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Pip-INstallable Dockerized Applications

Project description


Pip-INstallable Dockerized Applications

pinda is designed to deliver dockerized versions of software packages that have a user interface that is as identical as possible to what would be available if the package was installed in the conventional way.

For example, to install Gromacs version 2018:

% pinda install gromacs 2018

Once the installation is complete, you will find the 'gmx' command in your path.


Easiest via pip:

% pip install pinda


To see a list of packages available via pinda:

% pinda list
  amber      16         Amber and AmberTools version 16
  amber      18         Amber and AmberTools version 18
  ambertools 16         AmberTools version 16
  ambertools 18         AmberTools version 18
* gromacs    2018       Gromacs version 2018
  gromacs    2018-cuda  Gromacs version 2018 with CUDA support
* obabel     2.4.1      Open Babel version 2.4.1
  vina       1.1.2      AutoDock Vina and selected AutoDock Tools

Packages that you have already installed are asterisked.

NOTE: Because of license restrictions you may find that you can't actually run certain packages (e.g. Amber) - see here for some help on this.

To install a package:

% pinda install ambertools 18

To uninstall a package:

% pinda uninstall obabel 2.4.1


You need to have Docker installed on your machine. The containerised versions of the applications can only 'see' files that are in the directory a command in invoked from, or a subdirectory of this, so for example:

% gmx mdrun -s bpti.tpr # This is fine
% gmx mdrun -s ../bpti.tpr # This won't work


Charlie Laughton


BSD 3-clause

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