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alemg
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updated docker image with CRAN install
1 parent 05fda8c commit b9e7776

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Lines changed: 138 additions & 3 deletions

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‎docker/Dockerfile‎

Lines changed: 9 additions & 3 deletions
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@@ -55,15 +55,16 @@ RUN apt-get update && apt-get install -y r-base
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# Copy requirements
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COPY install2.r .
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COPY installBioc.r .
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# Required package for install2.r
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RUN R -e "install.packages('docopt', dependencies=TRUE)"
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# Essential R dependencies
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RUN Rscript install2.r --error --skipinstalled \
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remotes \
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BiocManager \
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b64 \
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pak \
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ggplot2 \
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cli \
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DT \
@@ -72,8 +73,13 @@ RUN Rscript install2.r --error --skipinstalled \
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optparse \
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&& rm -rf /tmp/downloaded_packages
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# R dependencies from CRAN
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RUN R -e "pak::pak('agusinac/OmicFlow')"
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RUN Rscript installBioc.r --error --skipinstalled \
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rhdf5 \
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&& rm -rf /tmp/downloaded_packages
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RUN Rscript install2.r --error --skipinstalled \
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OmicFlow \
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&& rm -rf /tmp/downloaded_packages
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# Make autoFlow.R directly callable from /usr/local/bin
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RUN ln -s "$(Rscript -e 'cat(system.file("exec", "autoFlow.R", package = "OmicFlow"))')" /usr/local/bin/autoflow \

‎docker/installBioc.r‎

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#!/usr/bin/env r
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#
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# Install a package from BioConductor
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#
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# Copyright (C) 2020 - 2022 Dirk Eddelbuettel
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# Copyright (C) 2022 - 2022 Dirk Eddelbuettel and Pieter Moris
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#
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# Released under GPL (>= 2)
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## load docopt package from CRAN
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library(docopt)
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## default to first library location in .libPaths()
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libloc <- .libPaths()[1]
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## configuration for docopt
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doc <- paste0("Usage: installBioc.r [-l LIBLOC] [-d DEPS] [-n NCPUS] [-r REPO ...] [--error] [--skipinstalled] [-m METHOD] [--force] [--update] [-h] [-x] [PACKAGES ...]
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-l --libloc LIBLOC location in which to install [default: ", libloc, "]
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-d --deps DEPS install suggested dependencies as well [default: NA]
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-n --ncpus NCPUS number of processes to use for parallel install [default: getOption]
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-r --repo REPO additional repository to use [default: getOption]
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-e --error throw error and halt instead of a warning [default: FALSE]
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-s --skipinstalled skip installing already installed packages (takes priority over --force) [default: FALSE]
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-m --method METHOD method to be used for downloading files [default: auto]
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-f --force force re-download of packages that are currently up-to-date [default: FALSE]
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-u --update update old already installed packages [default: FALSE]
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-h --help show this help text
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-x --usage show help and short example usage")
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opt <- docopt(doc) # docopt parsing
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if (opt$usage) {
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cat(doc, "\n\n")
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cat("where PACKAGES... can be one or more BioConductor names. Functionality depends on
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package 'BiocManger' which has be installed.
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Examples:
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installBioc.r -l /tmp/lib S4Vectors # install into given library
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installBioc.r --update Biobase # install package and update older packages
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installBioc.r --deps NA --error --skipinstalled # install package without suggested dependencies,
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# throw an error on installation failure and skip
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# packages that are already present
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installBioC.r is part of littler which brings 'r' to the command-line.
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See http://dirk.eddelbuettel.com/code/littler.html for more information.\n")
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q("no")
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}
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if (!requireNamespace("BiocManager", quietly=TRUE)) {
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stop("Please install 'BiocManager' first, for example via 'install.r BiocManager'.", call.=FALSE)
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}
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## set repository to empty character vector if not supplied, since
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## this is the input expected by BiocManager::install(site_repository=)
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## (does not accept NA)
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## the custom repository must be a sub-repository of a main BioC_mirror
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## e.g. software: https://bioconductor.statistik.tu-dortmund.de/packages/3.15/bioc/
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## annotation: https://ftp.gwdg.de/pub/misc/bioconductor/packages/3.14/data/annotation
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if (opt$repo == "getOption") {
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opt$repo = character()
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}
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## check if dependencies need to be installed, see
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## https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages
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## the default, NA, means c("Depends", "Imports", "LinkingTo"), but not "Suggests"
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if (opt$deps == "TRUE" || opt$deps == "FALSE") {
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opt$deps <- as.logical(opt$deps)
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} else if (opt$deps == "NA") {
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opt$deps <- NA
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}
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## set the number of parallel processes to use for a parallel install of
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## more than one source package, see
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## https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/install.packages
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if (opt$ncpus == "getOption") {
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opt$ncpus <- getOption("Ncpus", 1L)
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} else if (opt$ncpus == "-1") {
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## parallel comes with R 2.14+
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opt$ncpus <- max(1L, parallel::detectCores())
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}
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## helper function to catch errors that could arise when package installation has failed
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## and to skip installation of packages that are already present (for BiocManager::install()
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## these would otherwise result in additional warnings)
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install_bioc <- function(pkgs, ..., error = FALSE, skipinstalled = FALSE) {
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e <- NULL
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capture <- function(e) {
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if (error) {
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catch <-
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grepl("installation of .* packages failed", e$message) ||
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grepl("is not available", e$message) ||
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grepl("had non-zero exit status", e$message) ||
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grepl("compilation failed for package.*", e$message) ||
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grepl("fatal error", e$message) ||
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grepl("No such file or directory", e$message)
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if (catch) {
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e <<- e
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}
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}
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}
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if (skipinstalled) {
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pkgs <- setdiff(pkgs, installed.packages()[,1])
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}
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if (length(pkgs) > 0) {
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withCallingHandlers(BiocManager::install(pkgs, ...), warning = capture)
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if (!is.null(e)) {
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stop(e$message, call. = FALSE)
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}
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}
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}
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## ensure installation is stripped
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Sys.setenv("_R_SHLIB_STRIP_"="true")
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## install requested packages using helper function
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## ask must be set to FALSE because user prompts do not appear when calling
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## R from the CLI, e.g.
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## `R -e 'BiocManager::install("Biobase", ask=TRUE, update=TRUE)'`
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## might warn that MASS is out of date, but would not show a user prompt
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install_bioc(pkgs = opt$PACKAGES,
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lib = opt$libloc,
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site_repository = opt$repo,
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update = opt$update,
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ask = FALSE,
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force = opt$force,
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dependencies = opt$deps,
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Ncpus = opt$ncpus,
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method = opt$method,
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error = opt$error,
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skipinstalled = opt$skipinstalled)

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