As announced earlier this year, Bioconductor is moving version control systems from SVN to Git.
- Software, experiment data, and workflow packages will be maintained as git repositories created to capture the full commit history of each package. (the commit history of the 'data_store' portion of data experiment packages will unfortunately not carry forward to git).
- Read-only (user) access for each package is available via https, e.g.,
- Read-write (developer) access for each package is available via ssh, e.g.,
git clone email@example.com:packages/SummarizedExperiment
- Developers MUST SHARE public key(s) with Bioconductor. The process for this during the beta phase is outlined below.
- The build system and other core infrastructure will use git.bioconductor.org as the canonical source after the transition.
- Developers may wish to independently clone and maintain github or other repositories to support their package. Developers are responsible for pushing changes from these cloned repositories to the canonical source.
- https://github.com/Bioconductor-mirror will be removed after the transition.
We are starting Beta testing now. We encourage as many people as possible to become beta-testers, either as users (via git clone https://...) or maintainers (via git clone git@...).
All software, data experiment, and workflow packages are available at
(read / write)
git clone firstname.lastname@example.org:packages/<package>
These are STATIC SNAPSHOTS of SVN. Developers are encouraged to commit to these repositories, but the commits are not propagated to svn and will be lost at the end of the beta phase.
For maintainers, Bioconductor needs your SSH public key. We have prepared a Google form for this
The form requires your Bioconductor provided SVN username, and your Github user name (to retrieve your public keys from https://github.com/<your-github-id>.keys, make sure this is valid for your github username) OR SSH key. Currently, the form is processed on an approximately daily basis, so there is a delay between credential submission and developer access.
(IMPORTANT) As a beta tester, we ask that you work through the 'scenarios' at
Package authors and maintainers, please take the extra measure to check that your package history is complete to July 4th, i.e commit history, files, folders and all Bioconductor components.
If you are new to Git or Github, there are learning materials online https://try.github.io
We encourage pull-requests on documentation. Please post other beta-test feedback from the experience with the new git server to the bioc-devel mailing list or to the support site.
Transition: on date T, tentatively July 31st.
- Until July 30th 2017:
Beta testing phase.
- July 26th 2017:
Developer day demo session on Bioconductor's GIT transition/usage going forward. (30-45 mins) Be sure to attend if you are at Bioc2017, Boston. Slides will be made public.
- T - 2: Final SVN snapshot of data experiment packages
No more SVN commits to Data Experiment packages.
- T: Day of transition.
All SVN commits to software, experiment data, and workflow repositories are stopped, forever.
Git repositories are updated to most recent svn version on day T.
(We estimate that this will take about 6 hours; no commits possible on either svn or git).
Git commits resume. Please make sure to commit to
- Only git sever commits moving forward.
This is an important step for the infrastructure of the project. If you have questions please reply to this email, i.e. to the bioc-devel mailing list or support site. If there are any issues with individual packages, make sure to list them out.
Bioconductor Core Team