Bioconductor SVN to GIT transition

This package provides functionality to allow for SVN - Git transition for the Bioconductor Project.

Goals

• Create a private git server with all Bioconductor packages, including commit history from each of the RELEASE branches and the devel branch.

Setup

• To participate in the current testing cycle, communicate a single ssh public key to this google form https://goo.gl/forms/eg36vcBkIUjfZfLe2. We will not be accepting keys via email.

Usage: clone, push, pull, etc.

• ALPHA testing. Remember, repositories are static snapshots of svn; they are not current, changes commited here are not propagated to svn, and will not be retained.

• Clone a package for read-only access

  git clone https://git.bioconductor.org/packages/<package>.git
  

or for read / write (appropriate permissions required)

    git clone git@git.bioconductor.org:packages/<package>

• See the branches available

  cd BiocGenerics
  git branch -a
  

• Checkout branch and see if the commit history is correct

  git checkout RELEASE_3_0
  git log
  

• Local commits

  ...
  git commit -m "alpha test" -a
  

• Push commits to writeable repositories (commits will be lost after testing phases are complete)

  git push
  

• (Non-core users): Fail to push changes on non-master or RELEASE_3_4 branch.

  git checkout RELEASE_3_3
  ...
  git commit -m "alpha test" -a
  git push    # fail
  

Usage: exploration

• Elementary browser interface available at

  https://git.bioconductor.org
  

• View R(ead) / W(rite) privileges

  ssh git@git.bioconductor.org info        # all packages
  ssh git@git.bioconductor.org info packages/BiocGenerics
  

Status

• [x] ssh-based read-only access to all repositories
• [x] ssh-based read-write access to selected repositories
• [x] public read-only access to all repositories
• [ ] experiment-data packages

Troubleshooting

SSH

ssh may have to choose between multiple keys. Resolve this with an entry in the plain-text ~/.ssh/config file, where identityfile disambiguates the key you'd like to use.

    host git-bioc
        user git
        hostname git.bioconductor.org
        port 22
        identityfile ~/.ssh/id_rsa

Use as git clone git-bioc:packages/BiocGenerics.