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!