conda

Set up your conda

For macOSX

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
export PATH="$HOME/miniconda/bin:$PATH"

For Linux

wget https://repo.continuum.io/miniconda/Miniconda3-3.7.0-Linux-x86_64.sh -O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
export PATH="$HOME/miniconda/bin:$PATH"

Configure proper channels

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

Create a conda environment

For instance, if you are interested on genome aligners, you can create an isolated environment with the following tools:

conda create -n aligners samtools bamtools star
conda activate aligners

start using the tools, then to log off:

conda deactivate

Updated on 19 Jun 2019