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This page describes how to use github, which is our version control system.

Create an account on

It's free. Write to the sysadmins asking to have access to our repositories, as in

Set up for ssh access

Go to and paste your public key in the box

Fork for Development

Go to Click "Fork" to create your own working copy On your development machine and set the the trunk as upstream:

git remote origin[YOUR_USERNAME_HERE]/DOCK.git
git remote remove upstream
git remote add upstream

After making some changes, save them locally on your machine:

git commit -m "I changed test/file-abc" test/file-abc


git commit -a -m "I changed all the files"

After a series of changes are ready to push remotely

git push

If these changes should be added to the master DOCK branch

Go to[YOUR_USERNAME_HERE]/DOCK.git Click "Pull Request" in the upper-right corner of the file listing Click "Click to create a pull request for this comparison" Add any additional notes you may want Press "Send pull request" If you are an administrator in the primary DOCK repository, click "Merge pull request" , add any comments wanted, then click "Confirm merge" and the changes will be added to the DOCK trunk To update your fork with the trunk

git pull upstream master
git push


  • best practices for when and how to branch/merge
  • when and how to create a new repository

Lab repositories

  • docking-org/DOCK - DOCK 3 series software, currently DOCK 3.7
  • docking-org/ZINC - ZINC database creation, curation, management and interface
  • docking-org/cluster - tools for managing a cluster
  • docking-org/internal- our private scripts not part of another distribution

Friends of the lab's repositories

  • rdkit/rdkit - The official sources for the RDKit library
  • ryancoleman/analysis-scripts - Some simple scripts for analyzing lists of data, both paired & unpaired.
  • madgpap/chembl_clippy - cross platform molecular structure rendering app
  • metamolecular/osra - Optical structure recognition software, OSRA source from