Package: blacktie
Welcome to Blacktie!==========================This package is functional but under heavy development so you may want to periodicallypull 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 theinput/output streams of the tophat/cufflinks workflow** into a single yaml based configfile and automate as much of everything else as possible so that once the config fileis filled out, **the entire process of analysing a multi-condition RNA-seq experiment canbe 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 atwadunn83@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/issuesBlacktie 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.714149Usage-----.. code-block:: noneusage: blacktie [-h] [--version][--prog {tophat,cufflinks,cuffmerge,cuffdiff,cummerbund,all}][--hide-logs] [--no-email][--mode {analyze,dry_run,qsub_script}]config_fileThis script reads options from a yaml formatted file and organizes theexecution of tophat/cufflinks runs for multiple condition sets.positional arguments:config_file           Path to a yaml formatted config file containing setupoptions 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 outthe command lines; however, do not send the commandsto the system to be run. 3) 'qsub_script': generatebash scripts suitable to be sent to a computecluster'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 docs0.2.0rc1--------*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.