I'm installing the bioconductor wrapper to ensembl-vep in a docker container, using conda. Here is my dockerfile:

FROM centos:centos7.2.1511

RUN echo " - Installing development tools ..." \
    && yum install -y yum-plugin-ovl \
    && yum groupinstall -y "Development Tools"

# Install miniconda to /miniconda
RUN curl -LO http://repo.continuum.io/miniconda/Miniconda3-4.5.12-Linux-x86_64.sh
RUN bash Miniconda3-4.5.12-Linux-x86_64.sh -p /miniconda -b
RUN rm Miniconda3-4.5.12-Linux-x86_64.sh
ENV PATH=/miniconda/bin:${PATH}

RUN conda update -n base -c defaults conda

RUN conda config --add channels bioconda
RUN conda config --add channels conda-forge

RUN conda install ensembl-vep=94.5 bioconductor-ensemblvep r-base openssl=1.0
ENV PATH "/miniconda/share/ensembl-vep-94.5-0:$PATH"

RUN localedef -i en_US -f UTF-8 en_US.UTF8

Calling vep from the command line works. I can tell that the vep path is indeed appended to my $PATH. However, when I start R and load ensembl-vep library(ensemblVEP), I get the following output indicating that R has not found the vep script (4th line from the bottom):

> library(ensemblVEP)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: VariantAnnotation
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:DelayedArray':

    type

The following object is masked from 'package:base':

    strsplit


Attaching package: 'VariantAnnotation'

The following object is masked from 'package:base':

    tabulate

variant_effect_predictor.pl or vep script not found. Ensembl VEP is not installed in your path.

Attaching package: 'ensemblVEP'

The following object is masked from 'package:Biobase':

    cache

This is a bit weird, as when I call Sys.getenv("PATH"), R does in fact seem to have my vep path:

PATH           /miniconda/share/ensembl-vep-94.5-0:/miniconda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

Any hints on what I should do to make the ensemblVEP R function pick up the vep function as installed on the host?

I looked at

> ensemblVEP:::.onAttach
function (libname, pkgname)
{
    msg <- paste0("variant_effect_predictor.pl or vep script not found. ",
        "Ensembl VEP is not installed in your path.")
    tryCatch(check <- system2("perl", .getVepPath(), stdout = TRUE,
        stderr = TRUE), error = function(e) packageStartupMessage(msg))
}

.onAttach() is run when the ensemblVEP package is attached to the search path (hmm, should probably be .onLoad()...). It looks like it's trying to run perl on .getVepPath() to validate that vep is installed. So I looked at

> ensemblVEP:::.getVepPath
function ()
{
    if (nchar(Sys.getenv("VEP_PATH")))
        return(Sys.getenv("VEP_PATH"))
    loc0 <- unname(Sys.which("variant_effect_predictor.pl"))
...

Stepping through this I find that the container does not have the system utility which, so this could be installed. Alternatively, it looks like I can set VEP_PATH, e.g,

[root@a78d5b8a19c0 /]# export VEP_PATH=/miniconda/share/ensembl-vep-94.5-0/vep
[root@a78d5b8a19c0 /]# R

I'm a docker novice, but I think that means adding the line

ENV VEP_PATH /miniconda/share/ensembl-vep-94.5-0/vep

to the Dockerfile.

It looks like the VEP_PATH environment variable is not document, and that the intended solution is to add which to the image; this should be reported to bioconda so that they can update their recipe.