Installation
set conda config channels to the right priorities:
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict
create a new conda environment with starfish:
conda create -c egluckthaler -n starfish python=3.8 starfish
make sure this environment is activated anytime you want to use starfish:
conda activate starfish
using apptainer:
apptainer pull starfish.sif oras://ghcr.io/egluckthaler/starfish:latest
or using singularity:
singularity pull oras://ghcr.io/egluckthaler/starfish:latest
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 and requires that the package bash-completion is installed):
if [ -f $(dirname "$(which starfish)")/../aux/bash-completion.sh ]; then
source $(dirname "$(which starfish)")/../aux/bash-completion.sh
fi
The R package gggenomes is used in some visualization commands and can be installed by visiting the gggenomes github page