github.com/3d-e-chem/3d-e-chem-vm

3D e-Chem Virtual Machine

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

• VirtualBox, https://www.virtualbox.org
• Vagrant, https://www.vagrantup.com

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:

Build

Requirements:

• Virtualbox, https://www.virtualbox.org/
• Packer, https://packer.io
• Enough disk space
  • Make sure temporary directory (/tmp by default on Linux) has enough space. Use TMPDIR environment variable to overwrite default location
• ova file ../Chemical-Analytics-Platform/output-virtualbox-iso/cap.ova from build phase of https://github.com/NLeSC/Chemical-Analytics-Platform

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:

• Vagrant cloud account, https://app.vagrantup.com/nlesc/boxes/3d-e-chem

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