How to install blacktie
- Download and install ActivePython
- Open Command Prompt
pypm install blacktie
Welcome to Blacktie!
This package is functional but under heavy development so you may want to periodically pull the latest code from the repo at git://github.com/xguse/blacktie.git.
For the LATEST version pull the 'develop' branch.
I seek collaboration and contributions to improve this tool.
PLEASE take it and run with it, but send me your progress!
Its goal is to simplify the integration of all the input/output streams of the tophat/cufflinks workflow into a single yaml based config file and automate as much of everything else as possible so that once the config file is filled out, the entire process of analysing a multi-condition RNA-seq experiment can be run with a single command.
I have not had time to fill in ALL the doc strings but updating them regularly.
(Current version of the docs can be found here: http://xguse.github.com/blacktie/)
If you want to use/contribute before the docs are complete, please feel free to contact me at firstname.lastname@example.org for guidance.
If you find issues, bugs, or have feature requests, please go here to submit them: https://github.com/xguse/blacktie/issues
To credit the use of blacktie please cite the poster using the DOI link provided.
Introducing Blacktie: a simpler way to do RNA-seq using Tophat/Cufflinks/CummeRbund. Augustine Dunn. figshare. http://dx.doi.org/10.6084/m9.figshare.714149
Release date: 2013-07-17
version number system adopted to conform to PEP386
- This is a hot fix to squash a bug described in github issue: https://github.com/xguse/blacktie/issues/10
- in short: on a Mac pprocess complained "AttributeError: 'module' object has no attribute 'poll'" when trying to set up a queue.
- the quick fix is to look for that exception and continue without pprocess if encountered to avoid the fatal exception.
Release date: 2013-05-15
- git tag: 'v0.2.1'
- added new script named blacktie-cummerbund to run cummeRbund
- added new class in calls.py 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/calls.py: - 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.
Release date: 2013-03-21
- git commit SHA digest: 9d7c02d5e7f4ec8970bb2291c3eb6ff8f4dbe542
- git tag: 'v0.1.1'
Release date: 2013-03-20
- git commit SHA digest: 808c11fb396c71af55ff690fa6f2e628e5ffd758
- git tag: 'v0.1-dev'
- First uploaded to PyPI
- This verion is still under active development.