Setting up
In this section, we are going to et up a simple bioinformatics programming environment, giving you the ability to write, run, and test your code. We will use this setup throughout the rest of the book. It will be a simple setup, but enough so you can get productive immediately with the bioinformatic coding environment.
Setting up your development environment is a crucial step in learning bioinformatics. Following the instructions in this section and make sure your setting up is working. If you have questions, ...
Make sure you have gcc/clang installed. If you are using Linux or MacOS, gcc or clang should be pre-installed on your system. If you want to install gcc on MacOS, you can use Homebrew to install specific version of gcc.
And you can find your installation of gcc at /usr/local/Cellar/gcc@7/.
To install xcode command line developer tools on MacOS, try:
You should also have Python >= 3.7 installed. The Python official website provides detailed information on how to install specific version of Python in your system. In the rest of the book, sample code will be tested on Python 3.7.4, which support most of the bioinformatics packages.
We will be installing running following softwares/tools:
Basic bioinformatics libraries:
Aligner:
If you are using Linux system, binary excutables should be available on Github. You may also want to build from source for convenience in developing your own programs.
If you are using MacOS, some libaries can be installed using Homebrew. For example,
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