From b150dddc4535b170b4e40940b4dfaf349d477db2 Mon Sep 17 00:00:00 2001 From: Vladimir Kiselev Date: Thu, 15 Oct 2020 09:29:55 +0100 Subject: [PATCH] Update Dockerfile --- Dockerfile | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/Dockerfile b/Dockerfile index ae2941b38..b46e81dc6 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,7 +7,8 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \ libncurses5-dev \ libncursesw5-dev \ procps \ - texlive + texlive \ + libv8-dev # Install FastQC RUN curl -fsSL http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.5.zip -o /opt/fastqc_v0.11.5.zip && \ @@ -42,7 +43,7 @@ RUN curl -fsSL http://downloads.sourceforge.net/project/subread/subread-1.5.1/su rm /opt/subread-1.5.1-Linux-x86_64.tar.gz # Install cutadapt and MAGIC and awscli (to download data) -RUN pip install cutadapt magic-impute awscli +RUN pip install cutadapt magic-impute awscli==1.16.14 # Install TrimGalore RUN mkdir /opt/TrimGalore && \ @@ -61,7 +62,7 @@ RUN curl -fsSL https://github.com/arq5x/bedtools2/releases/download/v2.27.1/bedt rm /opt/bedtools-2.27.1.tar.gz # install CRAN packages -RUN apt-get update && apt-get install -yq --no-install-recommends \ +RUN apt-get update && apt-get install -yq \ r-cran-devtools \ r-cran-tidyverse \ r-cran-pheatmap \ @@ -143,14 +144,17 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \ r-cran-mgcv \ r-cran-corrplot +# Set Rprofile for binary installs +RUN echo 'options(repos = c(REPO_NAME = "https://packagemanager.rstudio.com/all/__linux__/focal/latest"))' > /home/jovyan/.Rprofile + # Install other CRAN RUN Rscript -e 'install.packages(c("Seurat", "rJava", "umap", "bookdown", "cluster", "KernSmooth", "ROCR", "googleVis", "ggbeeswarm", "SLICER", "ggfortify", "mclust", "Rmagic", "DrImpute"))' # Install Bioconductor packages -RUN Rscript -e 'BiocManager::install(c("graph", "RBGL", "gtools", "xtable", "pcaMethods", "limma", "SingleCellExperiment", "Rhdf5lib", "scater", "scran", "RUVSeq", "sva", "SC3", "TSCAN", "monocle", "destiny", "DESeq2", "edgeR", "MAST", "scmap", "biomaRt", "MultiAssayExperiment", "SummarizedExperiment"))' +RUN Rscript -e 'BiocManager::install(c("graph", "RBGL", "gtools", "xtable", "pcaMethods", "limma", "SingleCellExperiment", "Rhdf5lib", "scater", "scran", "RUVSeq", "sva", "SC3", "TSCAN", "monocle", "destiny", "DESeq2", "edgeR", "MAST", "scmap", "biomaRt", "MultiAssayExperiment", "SummarizedExperiment", "beachmat", "DropletUtils"))' # install github packages -RUN Rscript -e 'devtools::install_github(c("immunogenomics/harmony", "LTLA/beachmat", "MarioniLab/DropletUtils", "tallulandrews/M3Drop", "hemberg-lab/scRNA.seq.funcs", "Vivianstats/scImpute", "theislab/kBET", "kieranrcampbell/ouija", "hemberg-lab/scfind"))' +RUN Rscript -e 'devtools::install_github(c("immunogenomics/harmony", "tallulandrews/M3Drop", "hemberg-lab/scRNA.seq.funcs", "Vivianstats/scImpute", "theislab/kBET", "kieranrcampbell/ouija", "hemberg-lab/scfind"))' # download data and extra files from S3 COPY ./poststart.sh /home/jovyan