Installation ============ Requirements ------------ The following python modules must be installed for blacktie to function properly: :: Mako>=0.7.3 PyYAML>=3.10 The following modules will provide useful but optional functionality: :: pprocess>=0.5 rpy2 Installing the latest version from the git repository ----------------------------------------------------- .. Note:: Git is a **very** useful tool to have installed and to know how to use. `Learn more here `_ and `try it out here `_. Clone the repo:: $ git clone git://github.com/xguse/blacktie.git Install with any unmet requirements using ``pip``: :: $ [sudo] pip install -r blacktie/requirements.txt blacktie Install using standard ``setup.py`` script: :: $ cd blacktie $ [sudo] python setup.py install Use ``pip`` to obtain the package from `PyPI `_ ------------------------------------------------------------------------------ :: $ [sudo] pip install blacktie Mako PyYAML pprocess Installing without using ``git`` or ``pip`` for the download ------------------------------------------------------------ After installing the requirements: :: $ wget https://github.com/xguse/blacktie/archive/master.zip $ unzip master.zip $ cd blacktie-master $ [sudo] python setup.py install Test to see whether the install worked -------------------------------------- To test whether your installation was successful, open a new terminal session and type the following command. :: $ blacktie You should see the help text for blacktie and it should look something like this: .. 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) If this worked, great!