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        "author": "Augustine Dunn",
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        "description": "Welcome to Blacktie!\n==========================\n\nThis package is functional but under heavy development so you may want to periodically\npull the latest code from the repo at git://github.com/xguse/blacktie.git.\n\nFor the **LATEST** version pull the 'develop' branch.\n\n**I seek collaboration and contributions to improve this tool.**  \n\n**PLEASE** take it and run with it, but send me your progress!\n\nIts goal is to **simplify the integration of all the\ninput/output streams of the tophat/cufflinks workflow** into a single yaml based config\nfile and automate as much of everything else as possible so that once the config file\nis filled out, **the entire process of analysing a multi-condition RNA-seq experiment can\nbe run with a single command.**  \n\nI have not had time to fill in ALL the doc strings but updating them regularly.\n\n(Current version of the docs can be found here: http://xguse.github.com/blacktie/)\n\nIf you want to use/contribute before the docs are complete, please feel free to contact me at \nwadunn83@gmail.com for guidance.\n\nIssue tracking\n--------------\nIf you find issues, bugs, or have feature requests, please go here to submit them: https://github.com/xguse/blacktie/issues\n\n\nBlacktie Poster\n------------------------\n\n\n.. raw:: html\n\t<iframe src=\"http://wl.figshare.com/articles/714149/embed?show_title=1\" width=\"568\" height=\"200\" frameborder=\"0\"></iframe>\n\n\nTo credit the use of blacktie please cite the poster using the DOI link provided.\n\n\t*Introducing Blacktie: a simpler way to do RNA-seq using Tophat/Cufflinks/CummeRbund*. Augustine Dunn. figshare.\n\thttp://dx.doi.org/10.6084/m9.figshare.714149\n\n\n\nUsage\n-----\n.. code-block:: none\n\n\tusage: blacktie [-h] [--version]\n\t                [--prog {tophat,cufflinks,cuffmerge,cuffdiff,cummerbund,all}]\n\t                [--hide-logs] [--no-email]\n\t                [--mode {analyze,dry_run,qsub_script}]\n\t                config_file\n\n\tThis script reads options from a yaml formatted file and organizes the\n\texecution of tophat/cufflinks runs for multiple condition sets.\n\n\tpositional arguments:\n\t  config_file           Path to a yaml formatted config file containing setup\n\t                        options for the runs.\n\n\toptional arguments:\n\t  -h, --help            show this help message and exit\n\t  --version             Print version number.\n\t  --prog {tophat,cufflinks,cuffmerge,cuffdiff,cummerbund,all}\n\t                        Which program do you want to run? (default: tophat)\n\t  --hide-logs           Make your log directories hidden to keep a tidy\n\t                        'looking' base directory. (default: False)\n\t  --no-email            Don't send email notifications. (default: False)\n\t  --mode {analyze,dry_run,qsub_script}\n\t                        1) 'analyze': run the analysis pipeline. 2) 'dry_run':\n\t                        walk through all steps that would be run and print out\n\t                        the command lines; however, do not send the commands\n\t                        to the system to be run. 3) 'qsub_script': generate\n\t                        bash scripts suitable to be sent to a compute\n\t                        cluster's SGE through the qsub command. (default:\n\t                        analyze)\t\n\n\n\n\n\nCredits\n-------\n\n- `Distribute`_\n- `Buildout`_\n- `modern-package-template`_\n\n.. _Buildout: http://www.buildout.org/\n.. _Distribute: http://pypi.python.org/pypi/distribute\n.. _`modern-package-template`: http://pypi.python.org/pypi/modern-package-template\n\n\n.. image:: https://d2weczhvl823v0.cloudfront.net/xguse/blacktie/trend.png\n  :alt: Bitdeli badge\n  :target: https://bitdeli.com/free\n\n\n.. This is your project NEWS file which will contain the release notes.\n.. Example: http://www.python.org/download/releases/2.6/NEWS.txt\n.. The content of this file, along with README.rst, will appear in your\n.. project's PyPI page.\n\nNews\n====\n\n0.2.1.2\n-----------\n*Release date: 2013-07-17*\n\n* version number system adopted to conform to PEP386\n* This is a hot fix to squash a bug described in github issue: https://github.com/xguse/blacktie/issues/10\n    * **in short:** on a Mac ``pprocess`` complained \"AttributeError: 'module' object has no attribute 'poll'\" when trying to set up a queue.\n    * the quick fix is to look for that exception and continue without ``pprocess`` if encountered to avoid the fatal exception.\n\n\n\n0.2.1\n---------\n*Release date: 2013-05-15*\n\n* git tag: 'v0.2.1'\n* added new script named blacktie-cummerbund to run cummeRbund\n* added new class in calls.py CummerbundCall to use blacktie-cummerbund script to add cummeRbund plots to blacktie script\n* checks for R and rpy2 installations\n* if cummeRbund R library not found, it walks you through installing it\n* ``src/blacktie/utils/calls.py``: - fixed _flag_out_dir() so that if the outdir has not been created yet it gracefully moves on\n* ``examples/blacktie_config_example.yaml``: - added cummerbund_options\n* ``requirements.txt``: - added rpy2\n* updated docs\n\n0.2.0rc1\n--------\n\n*Release date: 2013-04-19*\n\n* git tag: 'v0.2.0rc1'\n* Added support for handling biological replicates in cuffdiff runs.\n* Major changes to yaml config:\n    * condition_queue[index].group_id --> condition_queue[index].experiment_id\n    * addition of condition_queue[index].replicate_id to track replicate data\n    * condition_queue[index].name now represents description of an 'experiemental condition' and will be shared by replicates.\n\n\n0.1.1\n-----\n\n*Release date: 2013-03-21*\n\n* git commit SHA digest: 9d7c02d5e7f4ec8970bb2291c3eb6ff8f4dbe542\n* git tag: 'v0.1.1'\n\n\n0.1_dev\n-------\n\n*Release date: 2013-03-20*\n\n* git commit SHA digest: 808c11fb396c71af55ff690fa6f2e628e5ffd758\n* git tag: 'v0.1-dev'\n* First uploaded to PyPI\n* This verion is still under active development.",
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        "keywords": "scientific computing RNA-seq tophat cufflinks bowtie CummeRbund",
        "license": "GPL 3",
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