Installing FastQC for command line in MobaXTerm

Question

[pychase12]

I want to use FastQC in MobaXTerm. I have downloaded it and unzipped the folder, which the installation guide says should be sufficient for it to work. However running fastqc --help in Moba gives the error message "fastqc: command not found" and it is not in the list of packages. What step am I missing? Any help appreciated. I am running Windows 10.

[ATpoint]

You should read about Unix basics. You can only call a binary if it is in PATH, please google PATH, and please read the link from antonioggsousa. By the way, you do not install in MobaxTerm, it is just an interface to ssh to another machine or server, so you install on that remote machine.

[i.sudbery]

Actually MobaXterm wraps a pretty complete, if very stripped down, version of cygwin. It is probably possible to install fastqc in this cygwin instance, but its probably not pretty.

On the flip side, you can use the mobaXterm terminal to launch local windows jobs, but the fastqc script is a perl script, so you would need windows perl installed, and you'd need to work out how to make the fastqc script launch with the windows perl interpreter.

[ATpoint]

Ok, #til.

[antonioggsousa]

Did you read this installation guide for fastqc? https://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt

I don't have a Windows but it sounds that you should have one icon to click on. Fastqc runs both in command-line and as Graphical User Interface (this assuming that you've java and the right version installed - the dependency).

If you have done that, my guess is that you need to turn the file fastqc executable as it explains in the installation instructions: chmod 755 fastqc

After this you should be able to run it. Still it'll not be in your PATH meaning that you need to specify the directory to where it is the executable to run it (unless that you follow the instructions to make the fastqc available to your PATH): <folder-where-is-the-fastqc-executable>/./fastqc --help

I hope this helps,

António

[JC]

I far better to use WSL2

Answer 1

[i.sudbery]

there are two things going on here.

First, whatever the Fastqc documents might say, installing Fastqc as a system-wide available command involves more than just unzipping the directory and running.

Firstly, to run fastqc you need to do one of:

• be in the same directory as fastqc (the mobaXterm terminal starts in a virtual directory called /home/mobaxterm by default. You can find your c drive mounted under /cygdrive/c
• specify the full path to the fastqc executable e.g. /cygdrive/c/Users/USERNAME/Downloads/fastqc_11.9.0/FastQC/fastqc myfastq.fastq
• Have the directory that contains fastqc as part of your $PATH directory.

Secondly, the fastqc executable is actaully a perl script. It also assumes that perl is installed at /usr/bin/perl. This tells me that although the script makes nodes to windows, and claims it works, it was never really designed to be used in Windows.

MobaXterm is not a full linux environment, instead it is a minimal distribution of something called cygwin, which is a linux emulator. In theory it might be possible to install perl into this environment (indeed, apt-get install perl_base claims it is going to do so), but I don't know how well that will go in mobaXterm, or whether it will survive closing mobaXterm and opening it again.

A better solution for using command line fastqc on windows might be to use WSL (windows subsystem for linux) which is a full linux distribution that can run on your windows box.