conda-envs

definition files for my conda environments

See also my conda cheat sheet!

general instructions

Most environments can be installed with simple:

conda env create --file env.yml
# or
mamba env create --file env.yml

Some environments need special instructions, see below.

base envs (base-hpc.yml & base-pc.yml)

conda base env with two flavours - HPC and PC (aka remote and localhost, resp.)

Since these are base environments, they cannot be created using these files, as base already exists and conda will throw an error. Instead, these files can be used for updating the base env (e.g. after fresh install):

conda-env update -f base-*pc.yml  # --prune will remove unused dependencies

admixtools2 env (admix.yml)

install admixtools2 in a new conda environment

1. Create a new conda environment (shell)

Create a new environment as described in the conda docs, activate it, and start R:

# create environment
$ conda-env create -f admix.yml

# activate environment
$ conda activate admix

# start R
$ R

2. Install admixtools2 inside activated environment (R)

After launching R inside the new environment, install admixtools2 by running the following:

> remotes::install_github("uqrmaie1/admixtools", dependencies = TRUE)
# or with devtools
# devtools::install_github("uqrmaie1/admixtools", dependencies = TRUE)

Finally, import admixtools2:

> library(admixtools)

Have fun 😉