moving the lamppost

random musings of a molecular biologist turned code jockey in the era of big data and open science.

NEW RELEASE: Blacktie v0.2.1

I have released a new version of blacktie (0.2.1) which has a number of minor fixes and NOW INCLUDES cummeRbund SUPPORT!!!


Thanks and again please let me know what you think. I need your input to make blacktie better and easier to use.



One major change was introduced in v0.2.0rc1: the yaml config file was changed slightly to facilitate the inclusion of biological replicate data. So please take a look at the demo config file in the docs posted at:

This is the last time that this warning will be included.



Release date: 2013-05-15

  • git tag: ‘v0.2.1’
  • added new script named blacktie-cummerbund to run cummeRbund
  • added new class in CummerbundCall to use blacktie-cummerbund script to add cummeRbund plots to blacktie script
  • checks for R and rpy2 installations
  • if cummeRbund R library not found, it walks you through installing it
  • src/blacktie/utils/ - fixed _flag_out_dir() so that if the outdir has not been created yet it gracefully moves on
  • examples/blacktie_config_example.yaml: - added cummerbund_options
  • requirements.txt: - added rpy2
  • updated docs


Release date: 2013-04-19

  • git tag: ‘v0.2.0rc1’

  • Added support for handling biological replicates in cuffdiff runs.

  • Major changes to yaml config:
    • condition_queue[index].group_id –> condition_queue[index].experiment_id
    • addition of condition_queue[index].replicate_id to track replicate data
    • condition_queue[index].name now represents description of an ‘experiemental condition’ and will be shared by replicates.