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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 2019:

% pinda install gromacs 2019

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
  ambertools 16         AmberTools version 16
  ambertools 18         AmberTools version 18
* gromacs    2019       Gromacs version 2019
  gromacs    2019-cuda  Gromacs version 2019 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.

To install a package:

% pinda install ambertools 18

To uninstall a package:

% pinda uninstall obabel 2.4.1

For detailed information on a package:

% pinda info ambertools 18

AmberTools version 18

This pinda distribution provides the following commands:

    "sander"      : the Amber/Ambertools "sander" command
    "amber-shell" : drops you into a bash shell from which all other
                    AmberTools commands are accessible (e.g. tleap).

For full license and usage information, please visit



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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