questions when installing 'Ensembl VEP' and R package 'ensemblVEP'
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ycchang • 0
Last seen 3.2 years ago

Hi there,

Just wondering if anyone has used 'Ensembl VEP' or R package 'ensemblVEP' before? I've got some questions here. I am new to R package 'ensemblVEP', but when I first library it, I found in the instruction that I need to install the 'Ensembl VEP'. so I tried to install this via windows cmd.

when I tried to install itenter image description here I tried 'perl'. However, it returned "'which' is not recognized as an internal or external command, operable program or batch file."

then I tried to install with '--NO_HTSLIB' however in this way the R package cannot work well (error message can be seen below)

I just want to make my R package work, what should I do?

Got stuck here. really appreciate for your help.

Thank you so much for your time

R ensemblVEP gene annotation Variant Effect Predictor Ensembl VEP • 535 views
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the pic could be seen from here.

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According to this recent document, there is slightly different installation steps for windows, and also says that you will see this 'which' is not recognized as an internal or external command but to ignore it. documentation instructions See Page 13 "Using VEP for Windows" . According to that documentation this should be ignored and is okay to still use.

The package ensemblVEP requires the installation on Ensembl VEP. Ensembl VEP is really a system requirement. If installation issues persist you might have better luck opening an issue on their GitHub .


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