/usr/bin/env: eCLIP_repelement_SE_singleNode: No such file or directory

[sarahbonnin]

Hello,

I want to run the repetitive-element-mapping pipeline, but I am a little confused about how to technically do it.

I got the "example reference data for GRCh38 (hg38)", I updated the yaml file "repeat_mapping_SE.yaml" with all required paths, and I exported the bin, bin/perl, wf/, and cwl/ in my PATH.

As I try to run the yaml file, I get the following error: "/usr/bin/env: eCLIP_repelement_SE_singleNode: No such file or directory".
"eCLIP_repelement_SE_singleNode" is in the bin folder, but it doesn't seem to find it. I have to say I am not really familiar with running yaml files, so it might be something very obvious...

I also saw that there is a Docker image available, which I pulled but I would need some guidance on how to use it to run the pipeline (I know how to run Docker images but I'm not sure how this one can be used for the pipeline).

Could you please guide me through the steps to get the pipeline up and running?

Thank you so much!

[sarahbonnin]

Hello! I was wondering if someone could help me on this?

[byee4]

Hi,

It seems like either your PATH isn't set up to find "eCLIP_repelement_SE_singleNode", or perhaps the file isn't marked as an executable. If you update your path:

export PATH=repetitive-element-mapping/wf/:$PATH

and ensure that it is executable:

chmod +x wf/eCLIP_repelement_SE_singleNode

You should be able to find and run the shell script wrapper.