How to install FastQC? If you are fluent with the english language and the command line, you can consult the official documentation which gives you all the step to install the software.
If you are not, you can consult this page in Spanish or French. And if you want the detailed english version, stay here!
First of all, you have to go to the main page of FastQC software. Then click on « Download now » button which leads you few lines forward. Here, there is two solutions:
- You want to use FastQC with the graphic user interface. To do so, you have to select the FastQC file for your platform (Windows/Linux or Mac). You will then have an installer (with a graphic user interface) which allows you to easily install the program.
- If you want to use FastQC with the command line, you can download the « Source Code for FastQC » and follow the next instructions.
Installation from source code:
Once you have downloaded and unzipped the folder (named FastQC), you have to choose a location for this folder. For example, in my computer the folder is placed in /Users/pbertin/Bioinformatics/Programs/FastQC.
The FastQC executable is present as « fastqc » in the downloaded folder. In order to be able to use it, you have to give the execution permissions at the latter file with the command:
chmod +x fastqc
and then use a symbolic link in a PATH directory (Refer to the Linux command explanations page to know more about the PATH). As a note, the PATH contains directories and the executables present in these directories can be executed from anywhere on your machine. To do this, use the command:
sudo ln -s /Users/pbertin/Bioinformatics/Programs/FasQC/fastqc /usr/local/bin/fastqc
You have to adapt the command with you own FastQC path. This symbolic link allows you to execute FastQC from anywhere on you machine. You have a more detailed description of what a symbolic link is in the Indiana University page.
Bioinformatics 