Using Conda to install bioinformatics software

Using Conda to install bioinformatics software is often easier than traditional methods and helps manage dependencies efficiently. To install FastQC, HISAT2, Samtools, and featureCounts using Conda, follow these steps:

Step 1: Install Miniconda or Anaconda (if not installed)

If you don’t have Conda installed, choose between Miniconda (lightweight version) and Anaconda (includes a large number of packages by default). Installation instructions can be found on their respective websites.

• Miniconda: https://docs.conda.io/en/latest/miniconda.html
• Anaconda: https://www.anaconda.com/products/individual

For example, to install Miniconda, you can do the following:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Follow the on-screen prompts to complete the installation. You may need to reload your shell configuration by running source ~/.bashrc or reopening the terminal.

Step 2: Create a Conda Environment (optional but recommended)

Creating a Conda environment for your bioinformatics tools can prevent conflicts between software versions. To create and activate a new environment called bioinfo, execute:

conda create -n bioinfo
conda activate bioinfo

Step 3: Install the Packages

You can now install FastQC, HISAT2, Samtools, and featureCounts with Conda. The bioconda channel contains these packages, and we need to add it and the conda-forge channel, which contains additional required packages:

conda config --add channels bioconda
conda config --add channels conda-forge

Finally, install the software:

conda install -n bioinfo -c bioconda fastqc hisat2 samtools subread

Replace bioinfo with the name of the Conda environment you created, if different.

Each tool can be installed individually as well:

conda install -c bioconda fastqc
conda install -c bioconda hisat2
conda install -c bioconda samtools
conda install -c bioconda subread

After the installation is complete, you can activate the bioinfo environment with conda activate bioinfo anytime you want to use these tools. Since they are now installed in a Conda environment, they will not interfere with other versions that might be installed globally or in other environments on your system.

Note: Make sure that your Conda is up to date by running conda update -n base -c defaults conda before installing the packages. If you encounter any dependency-related issues while installing, searching for the most recent version or specifying a version number in the install command may resolve these problems.