Question: questions when installing 'Ensembl VEP' and R package 'ensemblVEP'
gravatar for ycchang
3 months ago by
ycchang0 wrote:

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

ADD COMMENTlink written 3 months ago by ycchang0

the pic could be seen from here.

ADD REPLYlink written 3 months ago by ycchang0

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 .

ADD REPLYlink modified 3 months ago • written 3 months ago by shepherl ♦♦ 1.6k
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