a streamlined interface to the popular tophat/cufflinks RNA-seq pipeline
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
Usage
-----
::
usage: blacktie [-h] [--prog {tophat,cufflinks,cuffmerge,cuffdiff,all}]
[--hide-logs] [--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
--prog {tophat,cufflinks,cuffmerge,cuffdiff,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)
--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
.. 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
====
0.1.1
-----
*Release date: UNRELEASED*
* Example news entry for the in-development version
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.
==========================
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
Usage
-----
::
usage: blacktie [-h] [--prog {tophat,cufflinks,cuffmerge,cuffdiff,all}]
[--hide-logs] [--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
--prog {tophat,cufflinks,cuffmerge,cuffdiff,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)
--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
.. 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
====
0.1.1
-----
*Release date: UNRELEASED*
* Example news entry for the in-development version
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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