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

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!

Start by reviewing repeat_mapping_SE.yaml, the bin/eCLIP_repelement_SE_singleNode entry point, and the available Docker image instructions. Reproduce the reported command-not-found error with the example GRCh38 data and document the required invocation and environment setup so the pipeline can be run successfully.