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
- specify the full path to the fastqc executable e.g.
- 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.