There are many ways to install software (packages) inside Linux. For this workshop, we will learn how to install using Method (1) and (4).

1. Pre-built package/software or also known as binary package.
   • Whenever possible, try to obtain a pre-built package or also known as binary package.
   • To install, you usually just need to extract (if it is compressed) and add it to your $PATH.
2. Install through package manager such as ‘apt’ or ‘yum’ or ‘dpkg’.
   • the main problem with this method is you are required to have admin privileges
   • in the QU-Azure HPC, normal user (non-admin privilege) will not be able to use this feature
   • if you have your own linux server or your own linux laptop/desktop, you can install software using this method
   • this will usually install the tools/software in the /usr/bin location
3. Install from source file
   • When binary package is not available and you do not have access to package manager, you can try to compile the source file.
   • compiling a source file refers to the process where human written programming language (e.g., C, C++, Java) is converted into a machine language that can be directly executed by a computer.
   • the process typically involves commands like
     • ./configure
     • make
     • make install
   • Once upon a time, this was the main method to install bioinformatics software for people who do not have admin privileges.
   • the main problem with this method is that you need to make sure all the libraries dependency are met
4. Install through Conda package manager
   • this is the latest way to install many bioinformatics software
   • Conda is a package manager (similar to Windows’s Add or Remove Programs)
     • To install Conda
       • sh Anaconda3-2024.02-1-Linux-x86_64.sh and follow the instructions
       • verify Conda has been installed by typing conda –version
   • It can install many packages using various ‘channels’. A channel refers to the location where Conda looks to download packages.
     • Add important Conda channels via conda config –append channels defaults anaconda bioconda conda-forge r
   • Example of channels that are most often associated with bioinformatics are:
     • defaults
     • conda-forge
     • bioconda
     • r
     • anaconda
   • To search for a package in Conda
     • use https://anaconda.org/
     • conda search replace-with-package-name
   • To install
     • conda install -c replace-with-channel-name replace-with-name-of-package
   • To add a channel
     • conda config –add channels replace-with-channel-name
   • To show channels
     • conda config –show
   • To create conda environment
     • conda create –name ENVIRONMENT_NAME
   • To activate conda environment
     • conda activate reads_pre_processing
   • To deactivate conda environment
     • conda deactivate

Adding software to $PATH

• open .bashrc file using vim
  • vim ~/.bashrc
• add the following line:
  • export PATH=”/path/to/conda/bin:$PATH”
• save the .bashrc file
• source the .bashrc file (sometime you need to exit the terminal)
  • source ~/.bashrc

What is bashrc file?

• The ~/.bashrc file is a script that runs every time you open a new terminal window (or a new shell). The “~” represents your home directory, and “.bashrc” is the name of the file. The dot before the file name means it’s a hidden file.
• The ~/.bashrc file is used to configure your shell. It can contain commands, shell aliases, functions, and variables.
• It’s often used to set environment variables, change the command prompt, set the default editor, and create shortcuts for commonly used commands.