I have installed TrimGalore and Cutadapt for Mac OSX but when I try to run TrimGalore I always get the error message:
Failed to execute Cutadapt porperly. Please install Cutadapt first and make sure it is in the PATH, or specify the path to the Cutadapt executable using --path_to_cutadapt /path/to/cutadapt
I know that I have installed cutadapt from following the instructions here: https://cutadapt.readthedocs.io/en/stable/installation.html#quick-installation
but how do I make sure that Cutadapt is in the path?
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james.galske •
I'd suggest the simplest is to make the Cutadapt path globally accessible by including it in your ~/.bashrc. Then TrimGalore will automatically find it within the path and run successfully.
Hope this helps!
Thank you for your help. I am awfully new to computers, do you know how I can include it in my ~/.bashrc ?
I'd suggest having a look at an example here.
You may follow the steps below:
Get the path of Cutadapt where it is installed by the command which cutadapt
Copy the path that you get from Step1 and add it to your ~/.bashrc file as
export PATH=$PATH:cutadapt_installation_path
Replace the cutadapt_installation_path with the path you get from which cutadapt command
Save the ~/.bashrc file and type source ~/.bashrc on the terminal
If cutadapt is running from any directory, then it is accessible globally.
Hope this helps!
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Add the location of
cutadaptdirectory to your$PATHby doingexport PATH=$PATH:/dir_containing_cutadapt.