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CONDA and MAMBA

Uninstalling miniconda

rm -rf ~/miniconda3/
rm -rf ~/.conda
rm  ~/.condarc

# remove the conda block from your ~/.profile or ~/.bashrc

Adding channels

conda config --append channels conda-forge

Your ~/.condarc should now be updated with conda-forge

Creating and removing environments

# creating a new environment
conda create --name my_env

# create a new environment and install new packages at once
mamba create -n cogent3 -c bioconda cogent3

# install many packages at the same time using a YAML file
conda env create -n my_env -f env.yml

# remove an environment
conda env remove -n my_env

# remove/uninstall a package from the current environment
conda remove package

Environments defined in .yaml files

name: signalp6
channels:
    - bioconda
    - conda-forge
    - defaults
dependencies:
    - pip
    - pip:
        - signalp6==6.0+g
variables:
    FUNANNOTATE_DB: '/scratch4/db/funannotate/'

Hence, you can also add pip dependencies in your yaml file Ensure that you have both -pip and -pip: in there!

The YAML file is thus also an excellent way to setup environment variables!

Search for packages

# search for packages
conda search -c bioconda <package>

# search for packages in already installed environments
conda search --envs <package>
mamba search --envs <package>

# get info of versions and build numbers of packages
conda search -c bioconda <package> --info
mamba search -c bioconda <package> --info

Install packages in pre-existing environments

# installing a packages in an environment
conda install -c bioconda -n <my_env> <package>=<version> <package>=<version>

# mamba is a lot faster at resolving environments!
mamba install -c bioconda -n <my_env> <package>=<version> <package>=<version>

Activate and Deactivate environments

conda activate <my_env>
conda deactivate

Listing packages and environments

# list all environments
conda env list

# list packages in current environment
conda list

# checkout the history of an environment
## package upgrades / downgrades, additions, removals etc
conda list -n <my_env> -r 
# -r is short for --revisions

# revert back to an older revision of the environment
conda install --revision=REVNUM
# where REVNUM is the revision number, for example 2
# this will create a new revision number in the revision history,
# so if you are in rev 3, but you would like to return to 2, doing so
# will yield rev 4, which should be identical to rev 2

# export name, channels and all packages of a current active environment
conda env export > environment.yaml
mamba env export > environment.yaml

Update packages

conda update <package>
mamba update <package>

Renaming a conda environment

As far as I know there is not a direct rename option, but it is possible to copy an old environment to a new environment with a new name, and then delete the old environment

conda activate old_environment_name
conda env export > environment.yml

Now edit the name of the environment in the YML file to the new name. Then

conda env create -f environment.yml --name new_environment_name

conda deactivate
conda env remove --name old_environment_name

Installing perl modules with conda

## install the module LWP:Simple
conda install perl-lwp-simple
## so essentially replace ':' in module name with '-',
## lower case everything, and add 'perl-'

If the above method doesn't work, because it may not be available on a conda channel, or you don't know the right name, try the following

## install cpanminus
conda install perl-app-cpanminus

## install the desired perl module
cpanm Color::ANSI::Util

## or
env PERL5LIB="" PERL_LOCAL_LIB_ROOT="" PERL_MM_OPT="" PERL_MB_OPT="" $CONDA_PREFIX/bin/cpanm Color::ANSI::Util

If you are working on a Mac, you may need to install xcode first. On the command line, run xcode-select --install

Check the conda environment's library to check if the modules are installed in the right place

l /Users/joran/miniconda3/envs/colorFastq/lib/perl5/site_perl/

# should inlude Color/ANSI/Util.pm