Conda Dependencies Codefest Report

April 7th 2016

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.

Conda Dependencies Codefest

List of tools (versions) added to Bioconda:

  1. Seqtk r-75
  2. Shaker
  3. EDirect
  4. PeptideShaker and SearchGUI
  5. OpenBabel
  6. BamHash
  7. Trf

List of tools in [WIP]:

  1. All perl packages on osx
  2. Bioconductor minfi

List of tools removed from .tt_blacklist in IUC

  1. Seqtk
  2. Vegan
  3. Art
  4. Macs2

Infrastructure:

  1. Automatic push from tested tools to the Test Tool Shed in tools-iuc and bgruenings galaxytools
  2. More strict dependency handling in Bioconda

Thanks to everyone who participated!

Rémi Marenco. Nitesh Turaga, and Björn Grüning