Perl related error

[mrkidd]

Hi all. How or where can i check if my code for Variant Effect Predictor (VEP) and vcf2maf in a Conda environment is correct? I am getting a Perl relocation error I am not familiar with Perl so I'm not sure how to proceed. Any suggestions or insights would be greatly appreciated!

 

[Emali_day]

That error usually comes from a mismatch in Perl libraries inside conda, check which Perl is being used in your environment. The VEP docker image can bypass these issues entirely if you want something more stable. Posting the exact error would help narrow it down.

 

[TropicalMe]

Check perl V to see what it's linked to, and if you're using conda, make sure VEP and vcf2maf are installed in the same env with the right Perl.

 

[TissueCrafter]

It's great advice! I faced a similar issue a while back while setting up VEP in Conda. I completely overlooked the fact that I had two different versions of Perl in separate environments. It took me ages to figure out that a dependency mismatch was the culprit behind the relocation error. Running `perl -V` helped me get to the bottom of it quickly. It's definitely a good idea to double-check your environment setup. I hope you sort it out soon

 

[Fantastic Mr. Fox]

@mrkidd sounds like what @TissueCrafter and @TropicalMe mentioned is on point, that relocation error usually comes down to mismatched Perl builds. If you are stuck, trying the VEP docker like @Emali_day suggested might save you a lot of time.