Genomic Data Analysis II

Conda quickly installs, runs and updates packages and their dependencies. Conda can create and switch between environments on your computer, resolving dependency conflicts that might arise due to package requirements.

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Install Packages

Let’s first activate the base environment for conda:

conda activate base

You should see the (base) prefix before your username on the terminal.

Now let’s install the package fastqc. First, look up the package in the Anaconda repository: https://anaconda.org/bioconda/fastqc.

conda install -c bioconda fastqc

or

conda install bioconda::fastqc

If we wanted to specify the version of the tool, we can ‘pin’ the version in the install command:

conda install bioconda::fastqc=0.11.9

To Do:

  1. Check that fastqc has been installed correctly by prompting the help message.
  2. Check where fastqc was installed (hint: use whereis).

YAML file

We have seen how simple it is to install tools using the conda install command.

In reality, we will want to install multiple packages at once for an analysis and create a clean environment for the packages. This can be simplified using a .yml file. The strucutre of a .yml file is:

  1. Name: The name of the environment to be created.
  2. Channels: Specifiy which channels conda should search when attempting to install packages.
  3. Dependencies: Which packages you want to install (supports pinned version numbers).

In this weeks tutorial we want to create an environment for the quality control of sequencing reads. We will need fastqc and multiqc to generate HTML reports of sequencing statistics and a tool to perform adapter trimming and read filtering.

Choosing a trimming tool is highly subjective however, I like the flexibility of bbduk, part of the bbtools suite.

Please save the below block as week1.yml.

name: QC
channels:
  - agbiome
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - fastqc
  - multiqc
  - bbtools

To create a conda environment using the .yml file, run the following command in the terminal:

conda env create -f week1.yml && conda clean -a

Conda should install the three packages under the environment QC.

To Do:

  1. Activate the environment.
  2. Check all 3 tools have been installed correctly.
  3. Print the path of the environments bin.
  4. Export the environment using conda env export > QC.yml.