Conda guide (updated)

Conda guide (updated)

Updated conda installation instructions

Conda is a work in progress, and the best practices evolve quickly. This is my current recommended best practice, aimed at avoiding conflicts among packages, and preventing the need for total reinstallations.

Fresh installation

Download the latest Miniconda3 and install into your home directory.

# download latest 64-bit Py3 installation
# install in batch mode
bash Miniconda3-latest-Linux-x86_64 -b 

If conda is not yet in your path (e.g., this is your first time installing) then add it your path by calling:

~/miniconda3/condabin/conda init

Create a working environment

It is best not to install additional packages into your base environment. Instead, create one or more environments. I’ll create an environment using Python 3.7 since 3.8 is not yet widely supported.

conda create -n py37 Python=3.7
conda activate py37

Add conda-forge as your constant default channel

Remember that the order in which you list channels is important, since the they are checked in order to choose priority. It is best to install all packages from the same channel as much as possible to reduce conflicts. Conda-forge is the most expansive channel that also has the latest updates. Even if you need to install a package that is on bioconda, it is best to list conda-forge before bioconda so that any dependencies of the bioconda package will be pulled in from conda-forge.

conda config --add channels conda-forge
conda config --set channel_priority true

Installation of local software

When you are doing development you often want to install software locally with pip so that you can incorporate changes in your code instantly into your development environment. I recommend doing this with the option --no-deps like below to ensure you do not accidentally install dependencies with pip, since this can cause conflict problems. Here is an example with ipyrad cloned from github.

# install ipyrad from conda to get all dependencies
conda install ipyrad -c conda-forge -c bioconda

# clone the ipyrad repo to get git development version
git clone

# cd into the repo
cd ipyrad/

# do local pip install (-e) with --no-deps 
pip install -e . --no-deps