Home

Help pages

• Managing your Bioc code on hedgehog and github
• Preserve the original git committer in a dcommit

Frequently Asked Questions

• Create a new Bioconductor repo at github
• Watch a repo
• Delete a repo
• Setup your computer for git
• Clone a remote repo onto your computer
• Using ssh keys
• Overview of basic operations
• Add a user to a team
• Teams: setup & configuration
• Clone a Bioc SVN repository into a git & github repo
• Commit git-tracked changes back to Bioc SVN

About

The main goals of this repository is to promoted the usage of git and github as a support for Bioconductor package development:

1. Use github to promote wider collaboration between Bioconductor developers.

An example - BiocParallel Bioconductor facilities for parallel evaluation

2. Use github for all (or at least most) mentored projects.

Some examples

• VCF_projects for variant calling
• msGUI - a simple GU interface for MS data

3. Encourage those who use and prefer github to update to Bioc's svn early and often

When it becomes close to Bioc release times, lots of changes get often checked in that had been tracked in github. This can cause a flurry of last-minute fuss for developers and Bioc administrators. We want to encourage those package developers to keep the hedgehog svn repository synced up to scale those flurries back to a more comfortable level.

4. Provide help to all of us when we get confused.

If you have any ideas or requests that could streamline the (collaborative) development of Bioconductor packages, do not hesitate to get in touch via the Bioc-devel mailing list or file an issue.

Other tutorials

• Karl Broman's minimal tutorial on git and github.