Day 2 - Breakout 04

Conda Create Exercise (breakout)

15 Minutes

We’ve covered the basics of Conda, including how to create environments, as well as activate and deactivate them. We’ll use those same ideas in this exercise to create a conda environment with all of the software that we’ve used so far.

In this exercise, we’ll use a special tool that enhances Conda, called Mamba. It is used for environment creation, so you will use it in place of conda create in this exercise.

Instructions:

• One group member should share their screen in the breakout room. If nobody volunteers, a helper may randomly select someone.
• The group members should discuss the exercise and work together to find a solution.
• When a solution is found DO NOT have all users create the environment. Instead, choose only a few learners in each group to complete this exercise. We do not want to overwhelm the AWS instance.

• Use mamba to create an environment with all of the software that we used today:
  • cutadapt
  • fastqc
  • multiqc
  • star
  • rsem
• Use two channels when building the environment:
  • conda-forge
  • bioconda

Hint: The tool mamba is a drop-in replacement for conda create and similar commands. It is powerful and fast, which allows us to easily replicate our whole environment from today. conda create can be very slow or uncooperative when creating environments with certain software combinations, and mamba helps us get around that in this case. The command is exactly the same as a conda create command, e.g.:

mamba create -n <env-name> -c <channel> <package1> ...

Solution - Conda Create Exercise

# Create a conda environment with Cutadapt, FastQC, MultiQC, STAR, and RSEM.
mamba create -n RSD_environment -c conda-forge -c bioconda cutadapt fastqc multiqc star rsem
# Activate the environment and use which to check for software presence
conda activate RSD_environment
which cutadapt
which fastqc
which multiqc
which STAR
which rsem-calculate-expression
# Deactivate the environment
deactivate