Installing Bioconductor packages in Docker
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adklts • 0
@adklts-21974
Last seen 4 days 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 • 76 views
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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

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@konstantinos-yeles-8961
Last seen 14 hours 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!

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