Installation

Table of Contents

1. Main workflow and dependencies
2. Additional dependencies

Main workflow and dependencies

start by cloning the latest version of this github repository:

git clone https://github.com/egluckthaler/starfish.git
cd starfish/

then use conda to install other dependencies into a new, dedicated environment:

conda env create --file starfish.yml

activate the new conda environment anytime you want to use starfish:

conda activate starfish

starfish uses a customized version of cnef by Ayad et al. 2017

download a modified version of CNEFinder:

git clone https://github.com/egluckthaler/CNEFinder_starfish.git
./pre-install.sh

If using a linux machine, compile CNEFinder as follows:

make -f Makefile

If using Mac OS, compile CNEFinder as follows:

brew install gcc --without-multilib
make -f Makefile_M

finally, add the following lines to your $HOME/.bash_profile:

export PATH=$PATH:$HOME/starfish/
export PATH=$PATH:$HOME/starfish/CNEFinder/

starfish comes with a command auto-completion, which can be activated by adding these additional lines to your $HOME/.bash_profile:

if [ -f $HOME/starfish/util/bash-completion.sh ]; then
    source $HOME/starfish/util/bash-completion.sh
fi

Additional dependencies

The R package gggenomes is used in some visualization commands and can be installed by visiting the gggenomes github page