docker image for nextflow pipeline

[rbtoscan]

Hi,

I want to run some TCGA queries using TCGAbiolinks package inside my nextflow pipeline. Is there a recommended dockefile to make use in this case?

I tried this but it didn't work. the TCGAbiolinks is not found once I run 'library("TCGAbiolinks")' in my script.

FROM r-base:4.2.2
    RUN R -e "install.packages('dplyr',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('SummarizedExperiment',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('biomaRt',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('readr',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('DT',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('BiocManager',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('curl',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('openssl',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e 'BiocManager::install("GenomeInfoDbData")'
    RUN R -e 'BiocManager::install("TCGAbiolinks")'
    RUN R -e 'BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")'
    RUN R -e 'BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")'

Thank you.

Best Rodolfo

[tiagochst]

Some packages needs some dependencies to be installed.

FROM r-base:4.2.2
    RUN apt-get update && apt-get install -y libssl-dev libxml2-dev libcurl4-openssl-dev
    RUN R -e "install.packages('dplyr',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('SummarizedExperiment',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('biomaRt',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('readr',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('DT',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('BiocManager',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('curl',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e "install.packages('openssl',dependencies=TRUE, repos='http://cran.rstudio.com/')"
    RUN R -e 'BiocManager::install("GenomeInfoDbData")'
    RUN R -e 'BiocManager::install("TCGAbiolinks")'
    RUN R -e 'BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data")'
    RUN R -e 'BiocManager::install("BioinformaticsFMRP/TCGAbiolinks")'

You can build the image docker build -t docker-name .

And run docker run -it docker-name

If you tried to install TCGAbiolinks the errors would show up as shown below: