starfish_install.md

Setup starfish on DNAnexus ttyd using conda

Get miniconda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

bash Miniconda3-latest-Linux-x86_64.sh

export PATH="/home/dnanexus/miniconda3/bin:$PATH" # this is specific for DNAnexus ttyd

Set config channels

conda config --add channels bioconda

conda config --add channels conda-forge

conda config --set channel_priority strict

Create environment

conda create -c egluckthaler -n starfish python=3.8 starfish

Activate environment

conda activate starfish