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blacktie 0.2.1.2
A python wrapper for analysis of RNA-seq data with the popular tophat/cufflinks pipeline.

INSTALL>
pypm install blacktie

How to install blacktie

  1. Download and install ActivePython
  2. Open Command Prompt
  3. Type pypm install blacktie
 Python 2.7Python 3.2Python 3.3
Windows (32-bit)
Windows (64-bit)
Mac OS X (10.5+)
Linux (32-bit)
Linux (64-bit)
0.2.1.2 Available View build log
 
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Author
License
GPL 3
Dependencies
Lastest release
version 0.2.1.2 on Jan 9th, 2014

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 wadunn83@gmail.com for guidance.

Issue tracking

If you find issues, bugs, or have feature requests, please go here to submit them: https://github.com/xguse/blacktie/issues

Blacktie Poster

System Message: WARNING/2 (<string>, line 35)

"raw" directive disabled.

.. raw:: html
        <iframe src="http://wl.figshare.com/articles/714149/embed?show_title=1" width="568" height="200" frameborder="0"></iframe>

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
Usage

System Message: ERROR/3 (<string>, line 48)

Unknown directive type "code-block".

.. code-block:: none

        usage: blacktie [-h] [--version]
                        [--prog {tophat,cufflinks,cuffmerge,cuffdiff,cummerbund,all}]
                        [--hide-logs] [--no-email]
                        [--mode {analyze,dry_run,qsub_script}]
                        config_file

        This script reads options from a yaml formatted file and organizes the
        execution of tophat/cufflinks runs for multiple condition sets.

        positional arguments:
          config_file           Path to a yaml formatted config file containing setup
                                options for the runs.

        optional arguments:
          -h, --help            show this help message and exit
          --version             Print version number.
          --prog {tophat,cufflinks,cuffmerge,cuffdiff,cummerbund,all}
                                Which program do you want to run? (default: tophat)
          --hide-logs           Make your log directories hidden to keep a tidy
                                'looking' base directory. (default: False)
          --no-email            Don't send email notifications. (default: False)
          --mode {analyze,dry_run,qsub_script}
                                1) 'analyze': run the analysis pipeline. 2) 'dry_run':
                                walk through all steps that would be run and print out
                                the command lines; however, do not send the commands
                                to the system to be run. 3) 'qsub_script': generate
                                bash scripts suitable to be sent to a compute
                                cluster's SGE through the qsub command. (default:
                                analyze)

News

0.2.1.2

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.
0.2.1

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
0.2.0rc1

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.
0.1.1

Release date: 2013-03-21

  • git commit SHA digest: 9d7c02d5e7f4ec8970bb2291c3eb6ff8f4dbe542
  • git tag: 'v0.1.1'
0.1_dev

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.

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Last updated Jan 9th, 2014

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