Run Fastqc from terminal

Question

[filippoghmail]

Hi

I want to integrate fastqc in my pipeline but when I run the program from terminal is not working, I follow the instruction posted on git but the issue persist.

The step I followed are

Download FastQC.zip from https://github.com/s-andrews/FastQC/releases

Extract the content to my folder

I navigate to the folder and run:

> chmod +x fastqc

then

> sudo ln -s /Users/ghafil/Documents/BIOINFORMATICA/FastQC /usr/local/bin/fastqc

But when I check for:

> which fastqc

The output was

fastqc not found

When I run:

> ls -l /usr/local/bin/fastqc

The output is

lrwxr-xr-x  1 ghafil  admin  50 Aug 13 11:46 /usr/local/bin/fastqc -> /Users/ghafil/Documents/BIOINFORMATICA/FastQC

Can you help me? Thanks F

[brunobsouzaa]

What is the output when you run fastqc and, how are you running fastqc inside your pipeline?

[filippoghmail]

Thanks, you are right, I forgot to add the path to the binary

Answer 1

[antonioggsousa]

If you try:

sudo ln -s /Users/ghafil/Documents/BIOINFORMATICA/FastQC/fastqc /usr/local/bin/fastqc

I'm guessing that the binary is named fastqc and inside the folder FastQC. You need to specify it. Otherwise will not find it. Basically you are calling for the folder FastQC that of course is not executable.

If you check the installation guide you will see that: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt