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Conda is a general-purpose package and environment management system that allows to install, run, and update packages and their dependencies very efficiently. Besides, creating an environment using conda or miniconda in remote computer will enable one to install and manage softwares without need of sudo power. I usually create one conda environment for one research project, similar concept as creating a Rproject - if you are familiar to R programming, so that I can generate a summary file listing all the packages and their version used for a project or analyses.

Frequently used techniques to manage conda environment.

Managing conda

# Verify conda is installed
conda info

# Update conda package an denvironment
conda updata conda

Managing conda environments

# Create a new conda environment and install programs
conda create -y --name tnseqP python=3.6  # here tnseqP is the name of virtual environment, along with specific version of python
conda install -y --name tnseqP django=2.0.2
conda install -y --name tnseqP -c bioconda -c conda-forge anvio=5.0 diamond bwa

# Activate new environment
source activate tnseqP

# Installing additional packages to the new virtual environment
conda install -n tnseqP numpy=1.15

# Deactivate the virtual environment
source deactivate

# List the conda environments
conda env list
conda info --envs

# Make exact clone of an environment
conda create -n tnseqP --clone newtnseqP

Managing packages within a conda environment

# List the programs installed with a conda environment. 
conda list

# Search for a package available within a conda environment
conda search numpy

# Install a new package
conda install -n tnseqP pandas

# Update a package in the current environment
conda update pandas

# Install a package from a specific channel
conda install -c bioconda bwa

Removing packages or environments

# Removing a virtual environment
conda remove -n tnseqP -all
 
# Remove one package from the active environment
conda remove pandas

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Ravin Poudel
Computational Biologist (PostDoc)

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