Research

Question

[MARC]

Hello, I am trying to run a rnaseq workflow using systemPipeRdata. It seems that it calls trimmomatic which I install on my ubuntu laptop. however I get the following error:

Error: trimmomatic: command not found. Please make sure to configure your PATH environment variable according to the software in use.

It may be a simple manip to conduct but I don't really know which one.

any help would be welcome,

Marc

[Ram]

Title: Research

Is that the best you could do coming up with a succinct title that describes your problem well?

tag: trimmo_n_atic

Once again, please put more effort

Your Error message is not formatted in code formatting. Small steps like these go a long way in how readable your post is and how quickly you see relevant responses.

Answer 1

[GenoMax]

Please use a meaningful title for this post (you can edit the post to change it).

I am trying to run a rnaseq workflow using systemPipeRdata

This is not enough information about what software you are trying to run. Can you post a link to the workflow/pipeline?

Error: trimmomatic: command not found. Please make sure to configure your PATH environment variable according to the software in use.

If you have trimmomatic installed then you need to append the location to your $PATH by doing export PATH=$PATH:/path_to_trimmomatic_directory.