This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
Latest Version Dependencies status unknown Test status unknown Test coverage unknown
Project Description
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
------------------------


.. 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
-----
.. 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)





Credits
-------

- `Distribute`_
- `Buildout`_
- `modern-package-template`_

.. _Buildout: http://www.buildout.org/
.. _Distribute: http://pypi.python.org/pypi/distribute
.. _`modern-package-template`: http://pypi.python.org/pypi/modern-package-template


.. image:: https://d2weczhvl823v0.cloudfront.net/xguse/blacktie/trend.png
:alt: Bitdeli badge
:target: https://bitdeli.com/free


.. This is your project NEWS file which will contain the release notes.
.. Example: http://www.python.org/download/releases/2.6/NEWS.txt
.. The content of this file, along with README.rst, will appear in your
.. project's PyPI page.

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.
Release History

Release History

0.2.1.2

This version

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

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0.2.1

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Changelog content for this version goes here.

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0.2.0rc1

History Node

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Changelog content for this version goes here.

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0.1.1

History Node

TODO: Figure out how to actually get changelog content.

Changelog content for this version goes here.

Donec et mollis dolor. Praesent et diam eget libero egestas mattis sit amet vitae augue. Nam tincidunt congue enim, ut porta lorem lacinia consectetur. Donec ut libero sed arcu vehicula ultricies a non tortor. Lorem ipsum dolor sit amet, consectetur adipiscing elit.

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Download Files

Download Files

TODO: Brief introduction on what you do with files - including link to relevant help section.

File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
blacktie-0.2.1.2.tar.gz (31.9 kB) Copy SHA256 Checksum SHA256 Source Jul 17, 2013

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