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Add cipoc packages requested by users #11

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17 changes: 14 additions & 3 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# The base image is built with the create-builder-image.sh script.
ARG BASE_IMAGE=containers.renci.org/helxplatform/rstudio-base:focal-amd64
FROM $BASE_IMAGE as builder

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GitHub Actions / build-push-image

The 'as' keyword should match the case of the 'from' keyword 

FromAsCasing: 'as' and 'FROM' keywords' casing do not match
More info: https://docs.docker.com/go/dockerfile/rule/from-as-casing/

# Install a nodejs version that is newer than the one included in LTS version of Ubuntu.
# https://github.com/nodesource/distributions
Expand All @@ -21,7 +21,7 @@

# Drop build layer and copy the rstudio-server installed files to another
# layer.
FROM ubuntu:focal as base

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The 'as' keyword should match the case of the 'from' keyword 

FromAsCasing: 'as' and 'FROM' keywords' casing do not match
More info: https://docs.docker.com/go/dockerfile/rule/from-as-casing/

COPY --from=builder /usr/local/lib/rstudio-server /usr/local/lib/rstudio-server

Expand Down Expand Up @@ -53,8 +53,8 @@
RUN apt-get install -y libc6 libclang-dev libpq5 libsqlite3-0 libssl-dev \
lsb-release psmisc sudo

# Copy R script to install R packages.
COPY root/root/install-r-package.R /root/
# Copy R scripts to install R packages.
COPY root/root/install-r-package.R root/root/install-bioc-package.R /root/

# Install extra packages for ORDR-D.
# r-project packages available:
Expand Down Expand Up @@ -84,7 +84,18 @@
&& Rscript /root/install-r-package.R 'RPostgreSQL' \
&& Rscript /root/install-r-package.R 'tableone' \
&& Rscript /root/install-r-package.R 'tidyverse' \
&& Rscript /root/install-r-package.R 'xgboost'
&& Rscript /root/install-r-package.R 'xgboost' \
&& Rscript /root/install-r-package.R 'BiocManager' \
&& Rscript /root/install-r-package.R 'circlize' \
&& Rscript /root/install-r-package.R 'cluster' \
&& Rscript /root/install-r-package.R 'DescTools' \
&& Rscript /root/install-r-package.R 'hdnom' \
&& Rscript /root/install-r-package.R 'patchwork' \
&& Rscript /root/install-r-package.R 'readxl' \
&& Rscript /root/install-r-package.R 'rms' \
&& Rscript /root/install-r-package.R 'survival' \
&& Rscript /root/install-r-package.R 'survminer' \
&& Rscript /root/install-bioc-package.R 'ComplexHeatmap'

# Copy files used for rstudio configuration and starting rstudio-server.
COPY root /
Expand All @@ -111,4 +122,4 @@

WORKDIR /
USER $END_USER_USERNAME
CMD /start.sh

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JSON arguments recommended for ENTRYPOINT/CMD to prevent unintended behavior related to OS signals 

JSONArgsRecommended: JSON arguments recommended for CMD to prevent unintended behavior related to OS signals
More info: https://docs.docker.com/go/dockerfile/rule/json-args-recommended/
2 changes: 1 addition & 1 deletion config.env
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Expand Up @@ -11,7 +11,7 @@ IMAGE=focal

APP_NAME=rstudio-server
IMAGE_REPO=containers.renci.org/helxplatform
VERSION=v0.2.3
VERSION=v0.2.4

# These variables used when running the container.
CONTAINER_PORT=8787
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7 changes: 7 additions & 0 deletions root/root/install-bioc-package.R
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@@ -0,0 +1,7 @@
#!/usr/bin/env Rscript

args <- commandArgs(trailingOnly = TRUE)
package <- args[1]

BiocManager::install(package, dependencies=TRUE, update=FALSE, ask=FALSE)
stopifnot(package %in% installed.packages()[,'Package'])
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