Question

Installing Bioconductor packages in Docker

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adklts • 0

@adklts-21974

Last seen 10 weeks ago

Good afternoon. In my Dockerfile, I try to upload Bioconductor packages for a Shiny app in the following way

RUN Rscript -e 'install.packages("BiocManager")'

RUN Rscript -e 'BiocManager::install("rtracklayer")'

During the installation, I do not receive any kind of issue. But after when I try to run the app in Docker I receive a message that does not exist the packages of Bioconductor. Could anybody help me, please?

Bioconductor DOCKER RShiny • 397 views

ADD COMMENT • link updated 6 days ago by russ.bainer • 0 • written 5 months ago by adklts • 0

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Hi,

Can you tell me what base docker image you are using? (i.e you need a line in your Dockerfile like FROM bioconductor/bioconductor_docker:RELEASE_3_12 or some other image of that sort)

The information you have currently provided isn't enough for me to help you.

Best,

Nitesh

ADD REPLY • link 5 months ago nitesh.turaga 140

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Entering edit mode

Thank you very much for the answer I am uploading the dockerfile after the insert pf Bioconductor

# Base image https://hub.docker.com/u/rocker/
FROM rocker/shiny:latest

# system libraries of general use
## install debian packages
RUN apt-get update -qq && apt-get -y --no-install-recommends install \
    libxml2-dev \
    libcairo2-dev \
    libsqlite3-dev \
    libmariadbd-dev \
    libpq-dev \
    libssh2-1-dev \
    unixodbc-dev \
    libcurl4-openssl-dev \
    libssl-dev \
    coinor-libcbc-dev coinor-libclp-dev libglpk-dev


## update system libraries
RUN apt-get update && \
    apt-get upgrade -y && \
    apt-get clean

# copy necessary files
## app folder
COPY ./bms_msisuite ./app

# Docker inheritance
FROM bioconductor/bioconductor_docker:devel

RUN apt-get update
    RUN R -e 'BiocManager::install(ask = F)' && R -e 'BiocManager::install(c("rtracklayer", \
    "GenomicAlignments", "Biostrings", "SummarizedExperiment", "Rsamtools", ask = F))'
# install renv & restore packages
RUN Rscript -e 'install.packages("renv")'
RUN Rscript -e 'install.packages("devtools")'
RUN Rscript -e 'install.packages("shiny")'
RUN Rscript -e 'install.packages("shinyBS")'
RUN Rscript -e 'install.packages("ggvis")'
RUN Rscript -e 'install.packages("shinydashboardPlus")'
RUN Rscript -e 'install.packages("shinycssloaders")'
RUN Rscript -e 'install.packages("shinyWidgets")'
RUN Rscript -e 'install.packages("plotly")'
RUN Rscript -e 'install.packages("RSQLite")'
RUN Rscript -e 'install.packages("forecast", dependencies = TRUE)'
RUN Rscript -e 'install.packages("tsutils")'
RUN Rscript -e 'install.packages("readxl")'
RUN Rscript -e 'install.packages("tidyverse")'
RUN Rscript -e 'install.packages("knitr")'
RUN Rscript -e 'install.packages("knitcitations")'
RUN Rscript -e 'install.packages("nycflights13")'
RUN Rscript -e 'install.packages("Matrix")'
RUN Rscript -e 'install.packages("plotly")'
RUN Rscript -e 'install.packages("igraph")'
RUN Rscript -e 'install.packages("ggthemes")'
RUN Rscript -e 'install.packages("evaluate")'
RUN Rscript -e 'install.packages("psych")'
RUN Rscript -e 'install.packages("kableExtra")'
RUN Rscript -e 'install.packages("ggjoy")'
RUN Rscript -e 'install.packages("gtools")'
RUN Rscript -e 'install.packages("gridExtra")'
RUN Rscript -e 'install.packages("cowplot")'
RUN Rscript -e 'install.packages("ggrepel")'
RUN Rscript -e 'install.packages("data.table")'
RUN Rscript -e 'install.packages("stringr")'
RUN Rscript -e 'install.packages("rmarkdown")'
RUN Rscript -e 'install.packages("shinyjqui")'
RUN Rscript -e 'install.packages("V8")'
RUN Rscript -e 'devtools::install_github("ThomasSiegmund/D3TableFilter")'
RUN Rscript -e 'devtools::install_github("leonawicz/apputils")'
RUN Rscript -e 'devtools::install_github("Marlin-Na/trewjb")'

RUN Rscript -e 'devtools::install_github("dirkschumacher/ompr")'
RUN Rscript -e 'devtools::install_github("dirkschumacher/ompr.roi")'

RUN Rscript -e 'install.packages("ROI.plugin.glpk")'

RUN Rscript -e 'install.packages("shinydashboard")'
RUN Rscript -e 'install.packages("dplyr")'
RUN Rscript -e 'install.packages("dashboardthemes")'
RUN Rscript -e 'install.packages("shinyjs")'
RUN Rscript -e 'install.packages("magrittr")'
RUN Rscript -e 'install.packages("DT")'
RUN Rscript -e 'install.packages("rhandsontable")'
RUN Rscript -e 'renv::consent(provided = TRUE)'
RUN Rscript -e 'renv::restore()'



# expose port
EXPOSE 3838

# run app on container start
CMD ["R", "-e", "shiny::runApp('/app', host = '0.0.0.0', port = 3838)"]

ADD REPLY • link 4 months ago adklts • 0

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Has someone figured out what to do here? I'm having the same issue (apparent install while building the container, but the library cannot be subsequently loaded). I assume that this is a paths issue?

It seems like the responses below suggest changing to a BioC base image, but can someone please suggest a solution in situations where this is not practical?

ADD REPLY • link 6 days ago russ.bainer • 0

score 0 · Answer 1 · 2021-01-16

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Konstantinos Yeles ▴ 60

@konstantinos-yeles-8961

Last seen 6 days ago

University of Salerno, Salerno, Italy

Hello, adklts My way to do the installation of packages in a docker is like this:

    FROM bioconductor/bioconductor_docker:devel

    RUN apt-get update
    RUN R -e 'BiocManager::install(ask = F)' && R -e 'BiocManager::install(c("magick", \
    "tidyverse", "vroom", "VennDiagram", "PerformanceAnalytics", \
    "GO.db", "corrplot", ask = F))' && R -e 'tinytex::install_tinytex()'

Hope it helps!

ADD COMMENT • link 5 months ago Konstantinos Yeles ▴ 60

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Thanks for the answer. I follow instructions but when I run the app from docker I receive the follow message

shiny::runApp('/app', host = '0.0.0.0', port = 3838) Error in shinyAppDir(x) : No Shiny application exists at the path "/app" Calls:

<Anonymous> ... as.shiny.appobj -> as.shiny.appobj.character -> shinyAppDir Execution halted

This is related with bioconductor because when I deactivate the packages the app running.....but the point is that I need bioconductor. Have relation the position that i insert your code in dockerfile?

ADD REPLY • link 4 months ago adklts • 0

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Entering edit mode

Probably it has but as I haven't deployed a shiny app from docker yet I cannot say much. Have you tried to move :

# copy necessary files
## app folder
COPY ./bms_msisuite ./app

after the Bioconductor call?

# Docker inheritance
FROM bioconductor/bioconductor_docker:devel  

RUN apt-get update
    RUN R -e 'BiocManager::install(ask = F)' && R -e 'BiocManager::install(c("rtracklayer", \
    "GenomicAlignments", "Biostrings", "SummarizedExperiment", "Rsamtools", ask = F))'
# install renv & restore packages 
 .......
# copy necessary files
## app folder
COPY ./bms_msisuite ./app

ADD REPLY • link 4 months ago Konstantinos Yeles ▴ 60