Virtual machine with all software and sample data to run 3D-e-Chem Knime workflows
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README.md

3D e-Chem Virtual Machine

Build Status DOI

Scripts to create a Vagrant box using packer and ansible.

For available software/datasets/workflows inside Virtual machine see https://github.com/3D-e-Chem/3D-e-Chem-VM/wiki

Usage

Create a new directory and cd to it then start virtual machine with

vagrant init nlesc/3d-e-chem
vagrant up

Usage screencast on YouTube:

3D-e-Chem Virtual Machine screencast on YouTube

Build

Requirements:

packer build packer.json

Test

Add box to Vagrant with

vagrant box remove --force --all nlesc/3d-e-chem
vagrant box add --name nlesc/3d-e-chem --force packer_virtualbox-ovf_virtualbox.box

Then use steps described at Usage chapter in a new directory.

Push

Requirements:

Publish box on https://app.vagrantup.com/nlesc/boxes/3d-e-chem using the following steps:

  1. Create a new version
  2. Create a new provider
  3. Choose virtualbox as provider
  4. Choose Upload
  5. Press Continue to upload
  6. Upload the packer_virtualbox-ivf_virtualbox.box file generated by vagrant package
  7. Edit version
  8. Press Release version

Contributing

Please see CONTRIBUTING.md.

Cite

When using 3D-e-Chem-VM please cite one of the following:

  • Zenodo software release DOI
  • R. McGuire, S. Verhoeven, M. Vass, G. Vriend, I. J. P. De Esch, S. J. Lusher, R. Leurs, L. Ridder, A. J. Kooistra, T. Ritschel, C. de Graaf (2017). 3D-e-Chem-VM: Structural cheminformatics research infrastructure in a freely available Virtual Machine. Journal of Chemical Information and Modeling. doi: http://dx.doi.org/10.1021/acs.jcim.6b00686