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3d-e-chem-vm

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

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

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.8%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

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

Basic Info
Statistics
  • Stars: 16
  • Watchers: 5
  • Forks: 3
  • Open Issues: 5
  • Releases: 9
Created about 10 years ago · Last pushed over 7 years ago
Metadata Files
Readme Changelog Contributing License Code of conduct Citation

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

  • 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:

3D-e-Chem Virtual Machine 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

Owner

  • Name: 3D-e-Chem NLeSC project
  • Login: 3D-e-Chem
  • Kind: organization
  • Location: Amsterdam, The Netherlands

Software repositories for 3D-e-Chem project of Netherlands eScience Center

Citation (CITATION.cff) 

# YAML 1.2
# Metadata for citation of this software according to the CFF format (https://citation-file-format.github.io/)
cff-version: 1.0.3
message: If you use this software, please cite it as below.
title: 3D-e-Chem Virtual Machine
doi: 10.5281/zenodo.1170588
authors:
- given-names: Stefan
  family-names: Verhoeven
  affiliation: Nederlands eScience Center
version: 1.4.4
date-released: 2018-09-27
repository-code: https://github.com/3D-e-Chem/3D-e-Chem-VM
license: Apache-2.0

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Packages

  • Total packages: 1
  • Total downloads: unknown
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
proxy.golang.org: github.com/3d-e-chem/3d-e-chem-vm
  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 7.0%
Average: 8.2%
Dependent repos count: 9.3%
Last synced: 7 months ago