microbiomeMarker installation
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7 weeks ago

I have been trying to install microbiomeMarker following the instructions on the GitHub page on a docker image to run rstudio server as follow:

FROM rocker/tidyverse:4.2.1

RUN apt-get clean all && \
    apt-get update && \
    apt-get upgrade -y && \
    apt-get install -y \
        libhdf5-dev \
        libcurl4-gnutls-dev \
        libssl-dev \
        libxml2-dev \
        libpng-dev \
        libxt-dev \
        zlib1g-dev \
        libbz2-dev \
        liblzma-dev \
        libglpk40 \
        libgit2-dev \
        curl \
    && apt-get clean all && \
    apt-get purge && \
    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

RUN Rscript -e "devtools::install_github('haozhu233/kableExtra')"

RUN Rscript -e "install.packages(c('rmarkdown', 'tidyverse', 'BiocManager', \
'UpSetR', 'fastqcr', 'dplyr', 'pander', 'tidyr', 'remotes', \
'ggplot2', 'data.table', 'plyr',   'devtools', 'vegan', 'remotes', 'quarto', 'stats', \
'cluster', 'foreign', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'rpart'))"


RUN Rscript -e "BiocManager::install(c('phyloseq', 'DESeq2', 'ShortRead', 'Biostrings', \
'ComplexHeatmap', 'microbiome', 'dada2', 'DECIPHER', 'ngsReports'))"

RUN Rscript -e "devtools::install_github('jbisanz/qiime2R')"
RUN Rscript -e "library(qiime2R)"

RUN Rscript -e "BiocManager::install('mia')"
RUN Rscript -e "BiocManager::install('DirichletMultinomial')"
RUN Rscript -e "BiocManager::install('ANCOMBC')"
RUN Rscript -e "BiocManager::install('ALDEx2')"
RUN Rscript -e "devtools::install_github('https://github.com/YuLab-SMU/ggtree',dependencies = T)"
RUN Rscript -e "remotes::install_github('https://github.com/yiluheihei/microbiomeMarker/tree/RELEASE_3_18')"
#RUN Rscript -e "BiocManager::install('microbiomeMarker')"

RUN Rscript -e "BiocManager::install('karyoploteR')"
RUN Rscript -e "library(karyoploteR)"

WORKDIR /home/rstudio

I've run both remotes::install_github("yiluheihei/microbiomeMarker") and BiocManager::install('microbiomeMarker') when building the image. Docker build goes through, but microbiomeMarker is not installed on rstudio server. What's wrong in my Dockerfile? Any help is welcome.

install microbiomeMarker docker • 158 views
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