Conda Dependencies Codefest Report
The codefest started via hangouts at 10am EDT on Monday April 4, with around 8 participants. It was designed to be beginner friendly, which increased contribution from the community. 4 members of the galaxy community were added as contributors to the bioconda-recipe repository as a result of this hackathon.
The codefest started with Björn Grüning giving a small introduction to Conda and its channel Bioconda. Followed by how to create a new Conda recipe and the scripts involved in it. Members of the hack started by then picking up a simple tool and creating a Pull request against both the Tools-IUC and bioconda-recipes repositories on GitHub.
The main aim of the codefest was to get community members familiar with the Conda-Galaxy integration, and to remove tools from testing blacklist (shown below).
More details are here.
List of tools (versions) added to Bioconda:
- Seqtk r-75
- PeptideShaker and SearchGUI
List of tools in [WIP]:
- All perl packages on osx
- Bioconductor minfi
List of tools removed from .tt_blacklist in IUC
- Automatic push from tested tools to the Test Tool Shed in tools-iuc and bgruenings galaxytools
- More strict dependency handling in Bioconda
Thanks to everyone who participated!