"Installation" instructions
Clone this repository (or, if you don't want to install git, downloading and unzipping works too)
$ git clone https://github.com/kundajelab/av_scripts.git
Set the environment variable "UTIL_SCRIPTS_DIR" to point to the location of your cloned repository.
$ export UTIL_SCRIPTS_DIR=/path/to/av_scripts
Finally, add the 'exec' directory in av_scripts to your path:
$ export PATH=$PATH:$UTIL_SCRIPTS_DIR/exec
Additional convenience:
It is a good idea to add the export command to the end of your ~/.bashrc file (or create it if one doesn't exist) if you don't want to have to keep running it every time you log in. You can do this with:
$ echo "export UTIL_SCRIPTS_DIR=/path/to/av_scripts" >> ~/.bashrc
$ echo "export PATH=$PATH:$UTIL_SCRIPTS_DIR/exec" >> ~/.bashrc
Also, if you don't already have a ~/.bash_profile file, you should run the following command:
$ echo "source ~/.bashrc" >> ~/.bash_profile
(an explanation of the difference between ~/.bash_profile and ~/.bashrc is here: http://www.joshstaiger.org/archives/2005/07/bash_profile_vs.html)
Contact
Email avanti.shrikumar [at] gmail [dot] com or avanti [at] stanford [dot] edu with anything! My bioinformatics blog is here (search for the label av_scripts for posts relating to scripts in this repository: http://itinerantbioinformaticist.blogspot.com/2015/01/stratified-sampling-code-avscripts-repo.html)