- Overview
- Script to create/update Bioc branches
- Create GitHub repository of your package
- Commit changes to GitHub and Bioc SVN
- Update repository after a new Bioconductor release
This page contains my personal notes for maintaining Bioconductor packages on
GitHub and keeping them in sync with Bioconductor's SVN system using git svn.
Additional information can be fund on these sites:
Bioconductor provides a bash script called update_remotes.sh. This script
automates the creation, tracking and updates of the different development and
release branches from svn and the associated git mirrors. The script can
be downloaded from here or with curl
like this:
curl -O https://raw.githubusercontent.com/Bioconductor/mirror/master/update_remotes.shNote, the script can be located anywhere on a user's system.
Visit the static read-only mirror GitHub repository of your package. For a
package named REPO it would be this URL:
https://github.com/Bioconductor-mirror/REPO. Then fork it by clicking the
Fork button. This will create a copy of the repository in your GitHub
account. If needed turn on issue tracking for the new GitHub repository under
settings. Note, everything up to here needs to be done only once for each package.
Subsequently, clone the repository to your local machine and run the
update_remote.sh script to set up the git remotes:
git clone https://github.com/USER/REPO
cd REPO
bash /path/to/update_remotes.shThe following workflow uses cherry-pick to sync changes made in the master
branch to the devel branch. While less convenient, this method is more robust
than the git merge approach recommended on the Bioc Git Mirror page. For more
details, see here.
Changes to the development version should be made in the master branch of a package's GitHub repository. Those changes are then synced with the devel branch using git cherry-pick.
git branch # Lists all branches. The * marks the branch that is checked out.
git checkout master # Switch to master branch. This is where you make changes to the development version of the package.
git pull --rebase # Update local git repository. Rebase is important here since it avoids a merge which is part of a normal git pull
## <<< DO WORK HERE AND COMMIT/PUSH TO GITHUB AS USUAL >>>
git commit -am "some edits"; git push -u origin master
git checkout devel # Switch to devel which is the one from where you commit to SVN
git svn rebase # Gets latest changes from Bioc SVN
git commit -am "update" # Commits those changes
## git merge master # To minimize problems, avoid this merge step. Instead use cherry-pick method as shown in next two lines
git log master # Figure out what commit IDs to use and cherry pick them. Note, only the 7 first digits of listed numbers are needed and a range of commits can be given with 'ID1..ID2'
# git log --oneline --decorate --graph --all # Print history of your commit with branch pointers
git cherry-pick 4df7159 # Syncs commit from master to devel, here for commit ID 4df7159. This syntax spcifies range of commits: 4df7159..3gb7153
git svn dcommit # Now you should see changes on git mirror page
git commit -am "some edits"; git push -u origin devel
git checkout master # To be safe, switch back to master branchChanges to the release version should be made in a separate working branch of a
package's GitHub repository, just like under the developer branch. In the
following this branch is created by making a copy of the current release-x-x
branch and nameing it release-master. This name can be changed to anything.
Changes to release-master are then synced to the current release-x.x branch
using git cherry-pick (or git merge). The following assumes that the
current release branch is release-3.3.
# The following line creates a copy of release-3.3 and names this copy release-master. This needs to be done only once!
# git checkout release-3.3; git branch release-master release-3.3; git checkout release-master; git push -u origin release-master
git checkout release-master # Switch to release-master branch. This is where you make changes to the release version of the package
git pull --rebase # Update local git repository. Rebase is important here since it avoids a merge which is part of a normal git pull
## <<< DO WORK HERE AND COMMIT/PUSH TO GITHUB AS USUAL >>>
git commit -am "some edits"; git push -u origin release-master
git checkout release-3.4 # Switch to current release which is the one from where you commit to SVN
git svn rebase # Gets latest changes from Bioc SVN
git commit -am "update" # Commits those changes
## git merge release-master # To minimize problems, avoid this merge step. Instead use cherry-pick method as shown in next two lines
git log release-master # Figure out what commit IDs to use and cherry pick them. Note, only the 7 first digits of listed numbers are needed and a range of commits can be given with 'ID1..ID2'
# git log --oneline --decorate --graph --all # Print history of your commit with branch pointers
git cherry-pick 4df7159 # Syncs commit from release-master to release-x.x, here for commit ID 4df7159. This syntax spcifies range of commits: 4df7159..3gb7153
git svn dcommit # Now you should see changes on git mirror page
git commit -am "some edits"; git push -u origin release-3.4
git checkout release-master # To be safe, switch back to release-master branchTwice a year a new Bioconductor release becomes available. Those newly created
release branches need to be added to your local and remote GitHub repositories.
To add a new release branch, the easiest is to re-clone the repository from
GitHub and then re-run update_remotes.sh as outlined above under Create
GitHub repository of your package. After this the old local
copy of the repository can be deleted without loss of information assuming all
its content has been synced to the remote version on GitHub.