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Av scripts

A repository of handy scripts I've written since starting my PhD.

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"Installation" instructions

Clone this repository (or, if you don't want to install git, downloading and unzipping works too)

$ git clone

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:


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:


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: