Conda

Table of contents

  1. Create and Update Conda Environments
  2. To Completely remove Anaconda from your Computer

Create and Update Conda Environments

Example yaml file.

 name: h5n1day100
 channels:
   - bioconda
   - conda-forge
 dependencies:
   - r=3.5.1
   - snakemake=5.4.5
   - r-tidyverse=1.2.1
   - r-feather=0.3.2
   - r-venndiagram=1.6.20
   - r-tmod=0.40
   - r-biocmanager=1.30
   - bioconductor-biobase=2.42
   - r-logging=0.9_107

conda env create --file=environment.yaml

conda env update --file=environment.yaml

To activate conda environment conda activate h5n1day100

To deactivate conda environment conda deactivate

To remove conda environment conda env remove --name=<env name>

To Completely remove Anaconda from your Computer

To remove the configs:

conda install anaconda-clean
anaconda-clean --yes

Once the configs are removed you can delete the anaconda install folder, which is usually under your home dir:
rm -rf ~/anaconda3

Also, the anaconda-clean --yes command creates a backup in your home directory of the format ~/.anaconda_backup/<timestamp>. Make sure to delete that one also.

Now if you want to clean all, you will also have to delete the two last lines added to your .bash_profile. They look like:

# added by Anaconda3 5.2.0 installer
export PATH="/Users/ody/anaconda3/bin:$PATH"