From 893fca5ab2d42742bd8ada7ff694d0597d5e3107 Mon Sep 17 00:00:00 2001
From: rlyu <rlyu@svi.edu.au>
Date: Wed, 16 Oct 2019 14:27:21 +1100
Subject: [PATCH] add data folder and case study folder
---
Dockerfile | 24 ++++++++++++++----------
1 file changed, 14 insertions(+), 10 deletions(-)
diff --git a/Dockerfile b/Dockerfile
index 6b61659..f32c6a9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -17,6 +17,8 @@ RUN sudo apt-get update && apt-get install -yq --no-install-recommends gdal-bin
RUN sudo apt-get update && apt-get install -yq --no-install-recommends python3-gdal python3-numpy
RUN sudo add-apt-repository ppa:thomas-schiex/blender
RUN echo which gdal
+RUN sudo apt-get install -yq --no-install-recommends libudunits2-0 libudunits2-dev
+RUN sudo apt-get update && apt-get install -yq --no-install-recommends xorg libx11-dev libglu1-mesa-dev libfreetype6-dev
RUN sudo apt-get update && apt-get install -yq --no-install-recommends python-pip python3-pip && \
sudo pip3 install -U numpy
@@ -161,17 +163,10 @@ RUN apt-get update && apt-get install -yq --no-install-recommends \
# Install other CRAN
RUN Rscript -e 'install.packages(c("Seurat", "rJava", "umap", "bookdown", "cluster", "KernSmooth", "ROCR", "googleVis", "ggbeeswarm", "SLICER", "ggfortify", "mclust", "Rmagic", "DrImpute","Polychrome","future"))'
-RUN sudo apt-get update && apt-get install -yq --no-install-recommends xorg libx11-dev libglu1-mesa-dev libfreetype6-dev
# 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","EnsDb.Mmusculus.v79","slingshot","scds"))'
-RUN Rscript -e 'BiocManager::install(c("batchelor"))'
+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","EnsDb.Mmusculus.v79","slingshot","scds"))'
-RUN sudo apt-get install -yq --no-install-recommends libudunits2-0 libudunits2-dev
-
-RUN Rscript -e 'devtools::install_github(c("cole-trapnell-lab/leidenbase"))'
-
-RUN Rscript -e 'devtools::install_github(c("ChristophH/sctransform"))'
# install github packages
@@ -181,12 +176,21 @@ RUN Rscript -e 'install.packages(c("rsample"))'
RUN Rscript -e 'install.packages(c("Rcpp"))'
RUN Rscript -e 'install.packages(c("rstan"))'
RUN Rscript -e 'install.packages(c("gam"))'
+RUN Rscript -e 'devtools::install_github(c("ChristophH/sctransform"))'
+#RUN Rscript -e "install.packages('https://bioconductor.org/packages/3.9/bioc/src/contrib/Rhdf5lib_1.6.2.tar.gz', repos = NULL)"
+RUN Rscript -e "BiocManager::install('Rhdf5lib')"
+## downloading older version of HDF5Array due to installation problems with new version
+RUN ls -l /usr/local/lib/R/site-library/Rhdf5lib/lib/ && export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/usr/local/lib/R/site-library/Rhdf5lib/lib/" >> ~/.bashrc && echo $LD_LIBRARY_PATH
+RUN Rscript -e 'install.packages("https://bioconductor.org/packages/3.8/bioc/src/contrib/HDF5Array_1.10.1.tar.gz",repos = NULL,type = "source")'
+
+RUN Rscript -e 'BiocManager::install(c("DelayedMatrixStats","batchelor"))'
+RUN Rscript -e 'devtools::install_github(c("cole-trapnell-lab/leidenbase"))'
RUN Rscript -e 'devtools::install_github(c("cole-trapnell-lab/monocle3"))'
-RUN Rscript -e 'devtools::install_github(c("immunogenomics/harmony", "LTLA/beachmat", "MarioniLab/DropletUtils", "tallulandrews/M3Drop", "hemberg-lab/scRNA.seq.funcs"))'
+RUN Rscript -e 'devtools::install_github(c("immunogenomics/harmony", "LTLA/beachmat", "MarioniLab/DropletUtils", "tallulandrews/M3Drop", "hemberg-lab/scRNA.seq.funcs"),upgrade = "never")'
# install github packages
-RUN Rscript -e 'devtools::install_github(c("Vivianstats/scImpute", "theislab/kBET", "kieranrcampbell/ouija", "hemberg-lab/scfind"))'
+RUN Rscript -e 'devtools::install_github(c("Vivianstats/scImpute", "theislab/kBET", "kieranrcampbell/ouija", "hemberg-lab/scfind"),upgrade = "never")'
--
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