Question

Install old version of DESeq2

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Asma • 0

@asma-24876

Last seen 6 weeks ago

Canada

Hello,

I need to install an old version of DESeq2 and apeglm from 2019 in order to replicate some old results. I have tried to create a docker image using script below but DESeq2 does not install.

FROM bioconductor/bioconductor_docker:RELEASE_3_10
ENV DEBIAN_FRONTEND=noninteractive

# Install system dependencies for building Bioconductor packages
RUN apt-get update && apt-get install -y \
    libxml2-dev \
    libssl-dev \
    libcurl4-openssl-dev \
    libgit2-dev \
    zlib1g-dev \
    libncurses-dev \
    libbz2-dev \
    liblzma-dev \
    libpcre2-dev \
    build-essential \
    && rm -rf /var/lib/apt/lists/*

RUN R -e "install.packages(c( \
   'matrixStats', 'BiocParallel', 'DBI', 'RSQLite', 'XML', 'xtable', 'RCurl', \
   'RColorBrewer', 'ggplot2', 'Hmisc', 'Rcpp', 'RcppArmadillo', 'RcppEigen', \
   'RcppNumerical', 'locfit', 'emdbook' \
 ), repos = 'https://cran.microsoft.com/snapshot/2019-11-01')"

RUN R -e "BiocManager::install(c('DESeq2', 'apeglm'))"

Any recommendations for this?

apeglm Install DESeq2 version • 892 views

ADD COMMENT • link updated 9 weeks ago by James W. MacDonald 68k • written 9 weeks ago by Asma • 0

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Is there an error that occurs that can be shared?

ADD REPLY • link 9 weeks ago shepherl 4.2k

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To add to what Lori asks, this builds for me, using Dockerhub on Windows:

C:\Users\jmacdon\Desktop>docker build .
[+] Building 477.7s (8/8) FINISHED                                                                                                                                                                                      docker:desktop-linux
 => [internal] load build definition from Dockerfile                                                                                                                                                                                    0.0s
 => => transferring dockerfile: 838B                                                                                                                                                                                                    0.0s
 => [internal] load metadata for docker.io/bioconductor/bioconductor_docker:RELEASE_3_10                                                                                                                                                0.6s
 => [internal] load .dockerignore                                                                                                                                                                                                       0.0s
 => => transferring context: 2B                                                                                                                                                                                                         0.0s
 => [1/4] FROM docker.io/bioconductor/bioconductor_docker:RELEASE_3_10@sha256:dbe121d95a31eaa88a493ae66aa4035a236b2e37c69341ae74acb405e126f0c6                                                                                          0.0s
 => CACHED [2/4] RUN apt-get update && apt-get install -y     libxml2-dev     libssl-dev     libcurl4-openssl-dev     libgit2-dev     zlib1g-dev     libncurses-dev     libbz2-dev     liblzma-dev     libpcre2-dev     build-essentia  0.0s
 => [3/4] RUN R -e "install.packages(c(    'matrixStats', 'BiocParallel', 'DBI', 'RSQLite', 'XML', 'xtable', 'RCurl',    'RColorBrewer', 'ggplot2', 'Hmisc', 'Rcpp', 'RcppArmadillo', 'RcppEigen',    'RcppNumerical', 'locfit', 'emd  64.4s
 => [4/4] RUN R -e "BiocManager::install(c('DESeq2', 'apeglm'))"                                                                                                                                                                      411.7s
 => exporting to image                                                                                                                                                                                                                  0.8s
 => => exporting layers                                                                                                                                                                                                                 0.8s
 => => writing image sha256:32e9ee729a1c8af5e1bba37ed26cb3ce4edd7e862ed1c23ed0cf88778d829dc4                                                                                                                                            0.0s

View build details: docker-desktop://dashboard/build/desktop-linux/desktop-linux/s7l8bgffdqdq5xy45a5fkguis

ADD REPLY • link 9 weeks ago James W. MacDonald 68k