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Pip-INstallable Dockerized Applications

Project description

pinda

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.

pinda has been developed primarily to simplify the process of provisioning cloud compute resources, and at present it focusses on software tools useful for biomolecular simulation; but it may be used on other platforms and extended to other domains.

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.

Installation:

Easiest via pip:

% pip install pinda
% pinda update

Usage:

To see a list of packages available via pinda:

% pinda list
  NAMD       2.12       NAMD parallel molecular dynamics code, version 2.12
  ambertools 18         AmberTools version 18
  chimeratools 1.0.0      Molecular images via Chimera
  fpocket    3.0        FPocket version 3.0
  g_mmpbsa   5.1        g_mmpbsa for Gromacs 5.1
* gromacs    2019       Gromacs version 2019
  gromacs    2019-cuda  Gromacs version 2019 with CUDA support
  gromacs    5.1.4      Gromacs version 5.1.4
  gromacs    5.1.4-cuda Gromacs version 5.1.4 with CUDA support
  obabel     2.4.1      Open Babel version 2.4.1
  procheck   3.5.4      PROCHECK protein structure quality assessment tools
* propka     3.1.0      PROPKA version 3.1
  pymolqc    1.8.5.1    Python scripting interface to PyMOL without a GUI
  reduce     3.3.160602 REDUCE version 3.3.160602
* vina       1.1.2      AutoDock Vina and selected AutoDock Tools
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Packages that you have already installed are asterisked.

To install a package:

% pinda install ambertools 18
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To uninstall a package:

% pinda uninstall obabel 2.4.1
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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 http://ambermd.org

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Limitations:

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

Author:

Charlie Laughton charles.laughton@nottingham.ac.uk

License:

BSD 3-clause

Project details


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