datashield · DickPostma · Aug 26, 2026
diff --git a/molgenis-rock-possum/Dockerfile b/molgenis-rock-possum/Dockerfile
@@ -0,0 +1,40 @@
+#
+# Rock R Server Dockerfile with DataSHIELD Armadillo molgenis profile 
+#
+# https://github.com/datashield/docker-rock
+#
+
+# R 4.6.1, Rock 2.2.1
+FROM datashield/rock-base:6.3.5-R4.6.1
+
+ENV DSMEDIATION_VERSION=0.0.3
+ENV DSEXPOSOME_VERSION=2.0.9
+ENV DSTIDYVERSE_VERSION=v1.2.2
+ENV DSOMICS_VERSION=v1.0.19
+ENV DSMTL_VERSION=0.9.9
+ENV DSSURVIVAL_VERSION=v2.1.3
+ENV DSBASE_VERSION=6.3.5
+
+ENV ROCK_LIB=/var/lib/rock/R/library
+
+# Specify Labels
+LABEL dsMediation=${DSMEDIATION_VERSION}
+LABEL dsMTL=${DSMTL_VERSION}
+LABEL dsMSurvival=${DSSURVIVAL_VERSION}
+LABEL dsTidyverse=${DSTIDYVERSE_VERSION}
+LABEL dsExposome=${DSEXPOSOME_VERSION}
+LABEL dsOmics=${DSOMICS_VERSION}
+LABEL dsBase=${DSBASE_VERSION}
+RUN --mount=type=cache,target=/root/.cache/R \
+    --mount=type=cache,target=/tmp/downloaded_packages
+# Install new R packages
+RUN Rscript -e "remotes::install_github('datashield/dsMediation', ref = '$DSMEDIATION_VERSION', repos = c('https://cloud.r-project.org', 'https://cran.datashield.org'), upgrade = FALSE, lib = '$ROCK_LIB')" \
+ && Rscript -e "remotes::install_github('transbioZI/dsMTLBase', ref = '$DSMTL_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" \
+ && Rscript -e "remotes::install_github('datashield/dsSurvival', ref = '$DSSURVIVAL_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" \
+ && Rscript -e "remotes::install_github('molgenis/ds-tidyverse', ref = '$DSTIDYVERSE_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" \
+ && Rscript -e "BiocManager::install(c('bumphunter', 'missMethyl', 'rexposome'), update = FALSE, ask = FALSE, lib = '$ROCK_LIB')" \
+ && Rscript -e "remotes::install_github('isglobal-brge/dsExposome', ref = '$DSEXPOSOME_VERSION', repos = c('https://cloud.r-project.org', 'https://cran.datashield.org'), upgrade = FALSE, lib = '$ROCK_LIB')" \
+ && Rscript -e "BiocManager::install(c('Biobase', 'SNPRelate', 'GENESIS', 'GWASTools', 'GenomicRanges', 'SummarizedExperiment', 'DESeq2', 'edgeR', 'MEAL'), update = FALSE, ask = FALSE, lib = '$ROCK_LIB')" \
+ && Rscript -e "remotes::install_github('isglobal-brge/dsOmics', ref = '$DSOMICS_VERSION', upgrade = FALSE, lib = '$ROCK_LIB')" \
+ && Rscript -e "remotes::install_github('datashield/dsBase', ref = '$DSBASE_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" \
+ && chown -R rock $ROCK_LIB
diff --git a/molgenis-rock-possum/Dockerfile.bak b/molgenis-rock-possum/Dockerfile.bak
@@ -0,0 +1,32 @@
+#
+# Rock R Server Dockerfile with DataSHIELD Tulip Donkey profile
+#
+
+FROM datashield/molgenis-rock-base:4.1.0
+
+ENV DSMEDIATION_VERSION=0.0.3
+ENV DSEXPOSOME_VERSION=2.0.9
+ENV DSTIDYVERSE_VERSION=v1.2.2
+ENV DSOMICS_VERSION=v1.0.19
+ENV DSMTL_VERSION=0.9.9
+ENV DSSURVIVAL_VERSION=v2.1.3
+ENV DSBASE_VERSION=6.3.5
+
+ENV ROCK_LIB=/var/lib/rock/R/library
+
+LABEL dsMediation=${DSMEDIATION_VERSION}
+LABEL dsMTL=${DSMTL_VERSION}
+LABEL dsMSurvival=${DSSURVIVAL_VERSION}
+LABEL dsTidyverse=${DSTIDYVERSE_VERSION}
+LABEL dsExposome=${DSEXPOSOME_VERSION}
+LABEL dsOmics=${DSOMICS_VERSION}
+LABEL dsBase=${DSBASE_VERSION}
+RUN rm -f /etc/apt/sources.list.d/*arrow* || true
+RUN rm -f /etc/apt/sources.list.d/*apache* || true
+RUN apt-get update
+COPY install.R /tmp/install.R
+
+RUN --mount=type=cache,target=/root/.cache/R \
+    --mount=type=cache,target=/tmp/downloaded_packages \
+    Rscript /tmp/install.R \
+ && chown -R rock ${ROCK_LIB}
diff --git a/molgenis-rock-possum/LICENSE b/molgenis-rock-possum/LICENSE
diff --git a/molgenis-rock-possum/Makefile b/molgenis-rock-possum/Makefile
@@ -0,0 +1,43 @@
+#
+# Docker helper
+#
+export DOCKER_BUILDKIT=1
+
+docker_compose_file=docker-compose.yml
+no_cache=true
+name=datashield/molgenis-rock-possum
+tag=1.0.0
+
+# Build Docker image
+build-image:
+	docker build --no-cache=$(no_cache) -t="${name}:$(tag)" .
+
+push-image:
+	docker image push ${name}:$(tag)
+
+up:
+	docker compose -f $(docker_compose_file) up -d --remove-orphans
+
+down:
+	docker compose -f $(docker_compose_file) down
+
+stop:
+	docker compose -f $(docker_compose_file) stop
+
+start:
+	docker compose -f $(docker_compose_file) start
+
+restart:
+	docker compose -f $(docker_compose_file) restart
+
+pull:
+	docker compose -f $(docker_compose_file) pull --include-deps
+
+logs:
+	docker compose -f $(docker_compose_file) logs -f
+
+build:
+	docker compose -f $(docker_compose_file) build --no-cache
+
+clean:
+	rm -rf target
diff --git a/molgenis-rock-possum/README.md b/molgenis-rock-possum/README.md
@@ -0,0 +1,3 @@
+# docker-rock-tulip-donkey
+
+[Rock R server](https://www.obiba.org/pages/products/rock/) with DataSHIELD packages as described by [tulip-donkey](https://datashield.org/help/standard-profiles-and-plaforms).
diff --git a/molgenis-rock-possum/docker-compose.yml b/molgenis-rock-possum/docker-compose.yml
@@ -0,0 +1,22 @@
+services:
+  rock-tulip-donkey:
+    image: datashield/molgenis-rock-possum:1.0.0
+    #build: .
+    ports:
+      - ${PORT}:8085
+    environment:
+      - ROCK_ADMINISTRATOR_NAME=${ROCK_ADMINISTRATOR_NAME}
+      - ROCK_ADMINISTRATOR_PASSWORD=${ROCK_ADMINISTRATOR_PASSWORD}
+      - ROCK_MANAGER_NAME=${ROCK_MANAGER_NAME}
+      - ROCK_MANAGER_PASSWORD=${ROCK_MANAGER_PASSWORD}
+      - ROCK_USER_NAME=${ROCK_USER_NAME}
+      - ROCK_USER_PASSWORD=${ROCK_USER_PASSWORD}
+      - ROCK_ID=${ROCK_ID}
+      - ROCK_CLUSTER=${ROCK_CLUSTER}
+      - ROCK_TAGS=${ROCK_TAGS}
+      # for self-registration
+      #- ROCK_SERVER=${ROCK_SERVER}
+      #- ROCK_OPAL_SERVER=${ROCK_OPAL_SERVER}
+      #- ROCK_OPAL_TOKEN=${ROCK_OPAL_TOKEN}
+    volumes:
+      - ${PROJECT_HOME}/rock_home:/srv
diff --git a/molgenis-rock-possum/install.R b/molgenis-rock-possum/install.R
@@ -0,0 +1,76 @@
+rock_lib <- Sys.getenv("ROCK_LIB")
+
+repos <- c(
+  CRAN = "https://cloud.r-project.org",
+  DataShield = "https://cran.datashield.org"
+)
+
+options(repos = repos)
+Sys.setenv(PAK_SYSREQS = "false")
+
+# pak installeren indien nog niet aanwezig
+if (!requireNamespace("pak", quietly = TRUE)) {
+  install.packages(
+    "pak",
+    repos = "https://cloud.r-project.org",
+    lib = rock_lib
+  )
+}
+
+.libPaths(c(rock_lib, .libPaths()))
+
+# GitHub packages
+pak::pkg_install(
+  c(
+    sprintf(
+      "github::datashield/dsMediation@%s",
+      Sys.getenv("DSMEDIATION_VERSION")
+    ),
+    sprintf(
+      "github::transbioZI/dsMTLBase@%s",
+      Sys.getenv("DSMTL_VERSION")
+    ),
+    sprintf(
+      "github::datashield/dsSurvival@%s",
+      Sys.getenv("DSSURVIVAL_VERSION")
+    ),
+    sprintf(
+      "github::molgenis/ds-tidyverse@%s",
+      Sys.getenv("DSTIDYVERSE_VERSION")
+    ),
+    sprintf(
+      "github::isglobal-brge/dsExposome@%s",
+      Sys.getenv("DSEXPOSOME_VERSION")
+    ),
+    sprintf(
+      "github::isglobal-brge/dsOmics@%s",
+      Sys.getenv("DSOMICS_VERSION")
+    ),
+    sprintf(
+      "github::datashield/dsBase@%s",
+      Sys.getenv("DSBASE_VERSION")
+    )
+  ),
+  lib = rock_lib
+)
+
+# Bioconductor packages in één call
+BiocManager::install(
+  c(
+    "bumphunter",
+    "missMethyl",
+    "rexposome",
+    "Biobase",
+    "SNPRelate",
+    "GENESIS",
+    "GWASTools",
+    "GenomicRanges",
+    "SummarizedExperiment",
+    "DESeq2",
+    "edgeR",
+    "MEAL"
+  ),
+  update = FALSE,
+  ask = FALSE,
+  lib = rock_lib
+)
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		# docker-rock-tulip-donkey

		[Rock R server](https://www.obiba.org/pages/products/rock/) with DataSHIELD packages as described by [tulip-donkey](https://datashield.org/help/standard-profiles-and-plaforms).