Running fastqc

Question

[margo]

I am trying to run fastqc from my home directory using the command line. I do not have access to the root directory. I have downloaded fastqc zip file and unzipped it. When going into the FastQC directory, the following options are available:

Configuration,
LICENSE_JHDF5.txt
cisd-jhdf5.jar
net
uk
Help
README.txt
fastqc
org
INSTALL.txt
RELEASE_NOTES.txt
fastqc_icon.ico
run_fastqc.bat
LICENSE.txt
Templates
jbzip2-0.9.jar
sam-1.103.jar

However, when I try to run fastqc, an error message appears:

Command 'fastqc' not found, but can be installed with:
apt install fastqc
Please ask your administrator.

Is there something that I am doing wrong? How can I install fastqc in your home space as you don't have root on the server and run the programme?

[GenoMax]

Please use conda to install FastQC. No root privileges are needed for this method. You will need a working X11 install otherwise you will have to download the resulting html files for viewing on your local machine.

Use conda part of tutorial here: Creating workflows with snakemake and conda

conda create -n fastqc fastqc 
conda activate fastqc
fastqc your_fastq_file_list

[Trivas]

Yes, margo you downloaded the GUI version of FastQC. This isn't necessarily bad, you can drag and drop your fastq files into the gui, but doesn't lend itself to automation very well.

Answer 1

[Istvan Albert]

fastqc only requires java to be present, check the installation instructions here

https://raw.githubusercontent.com/s-andrews/FastQC/master/INSTALL.txt

as you can see if you have java running on your system, there is not much installation, to quote:

Actually installing FastQC is as simple as unzipping the zip file it comes in into a suitable location.

That's it.

Once unzipped it's ready to go.

[Angelina_G]

Hello, I did have java version "18.0.2.1" 2022-08-18, and I have downloaded the lastest version of FastQC zip file and unzipped it, after that I used cd to set the current directory into folder FastQC-0.11.9, then used fastqc command, but it still tells me -bash: fastqc: command not found. I tried the same approach on another java-based package picard and it worked, could you please help me point out what might have gone wrong? Thank you!

[GenoMax]

This is simply because the directory you have the fastqc wrapper script in is not in your $PATH. If you are in the directory with the script then you can simply run ./fastqc (to get the GUI) or ./fastqc *.fastq.gz (to run on command line).