Installation

Table of Contents

1. Main workflow and dependencies
2. Additional dependencies

Main workflow and dependencies

install via anaconda (recommended):

create a new conda environment:

conda create -n starfish python=3.8

make sure conda config channels have the right priorities:

conda config --add channels bioconda
conda config --add channels conda-forge

activate environment and install:

conda activate starfish
conda install -c egluckthaler starfish

make sure this environment is activated anytime you want to use starfish:

conda activate starfish

alternatively, install via git:

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

cd CNEFinder/
./pre-install.sh

compile CNEFinder as follows (only works for linux machines):

make -f Makefile

finally, add the following lines to your .bash_profile or .bashrc (replace the placeholder paths with the absolute paths to the requested directories on your machine):

export PATH=$PATH:/path/to/starfish/directory/bin/
export PATH=$PATH:/path/to/CNEFinder/directory/

starfish comes with a command auto-completion, which can be activated by adding these additional lines to your .bash_profile or .bashrc (note: will only work if starfish is accessible on the commandline as soon as you log in):

if [ -f $(dirname "$(which starfish)")/../aux/bash-completion.sh ]; then
    source $(dirname "$(which starfish)")/../aux/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