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feat: docker image size optimizations #16

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feat: docker image size optimizations #16

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24 changes: 24 additions & 0 deletions omicron-karma/.dockerignore
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Original file line number Diff line number Diff line change
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# Ignore common files that shouldn't be included in Docker build context
.git
.gitignore
README.md
LICENSE
Makefile
docker-compose.yml
*.md

# Ignore temporary files
*.tmp
*.temp
*~
.DS_Store
Thumbs.db

# Ignore logs
*.log

# Ignore IDE files
.vscode/
.idea/
*.swp
*.swo
57 changes: 30 additions & 27 deletions omicron-karma/Dockerfile
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Expand Up @@ -7,31 +7,34 @@
# R 4.5.0, Rock 2.1.1
FROM datashield/rock-base:6.3.3

ENV DSMEDIATION_VERSION=0.0.3
ENV DSEXPOSOME_VERSION=2.0.9
ENV DSTIDYVERSE_VERSION=v1.0.4
ENV DSOMICS_VERSION=v1.0.18-2
ENV DSMTL_VERSION=0.9.9
ENV DSSURVIVAL_VERSION=v2.1.3
ENV DSBASE_VERSION=6.3.3
# Set environment variables
ENV DSMEDIATION_VERSION=0.0.3 \
DSEXPOSOME_VERSION=2.0.9 \
DSTIDYVERSE_VERSION=v1.0.4 \
DSOMICS_VERSION=v1.0.18-2 \
DSMTL_VERSION=0.9.9 \
DSSURVIVAL_VERSION=v2.1.3 \
DSBASE_VERSION=6.3.3 \
ROCK_LIB=/var/lib/rock/R/library

ENV ROCK_LIB=/var/lib/rock/R/library

# Install new R packages
# dsMediation
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')"
# dsMTLBase
RUN Rscript -e "remotes::install_github('transbioZI/dsMTLBase', ref = '$DSMTL_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')"
# dsSurvival
RUN Rscript -e "remotes::install_github('datashield/dsSurvival', ref = '$DSSURVIVAL_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')"
# dsTidyverse
RUN Rscript -e "remotes::install_github('molgenis/ds-tidyverse', ref = '$DSTIDYVERSE_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')"
# dsExposome
RUN 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 = '$ROCK_LIB')"
# dsOmics
RUN Rscript -e "BiocManager::install(c('Biobase', 'SNPRelate', 'GENESIS', 'GWASTools', 'GenomicRanges', 'SummarizedExperiment', 'DESeq2', 'edgeR', 'MEAL'), update = FALSE, ask = FALSE, lib = '$ROCK_LIB')" \
&& Rscript -e "remotes::install_github('isglobal-brge/dsOmics', ref = '$DSOMICS_VERSION', upgrade = FALSE, lib = '$ROCK_LIB')"
# dsBase
RUN Rscript -e "remotes::install_github('datashield/dsBase', ref = '$DSBASE_VERSION', dependencies = TRUE, upgrade = FALSE, lib = '$ROCK_LIB')" && \
chown -R rock $ROCK_LIB
# Install new R packages in a single layer to reduce image size
RUN Rscript -e "install.packages('BiocManager', repos = 'https://cloud.r-project.org')" && \
# Install BiocManager packages first
Rscript -e "BiocManager::install(c('bumphunter', 'missMethyl', 'rexposome', 'Biobase', 'SNPRelate', 'GENESIS', 'GWASTools', 'GenomicRanges', 'SummarizedExperiment', 'DESeq2', 'edgeR', 'MEAL'), update = FALSE, ask = FALSE, lib = '$ROCK_LIB')" && \
# Install GitHub packages
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 "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 "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')" && \
# Clean up temporary files and caches to reduce image size
rm -rf /tmp/* && \
rm -rf /var/lib/apt/lists/* && \
rm -rf /root/.cache/R && \
Rscript -e "if (file.exists('/tmp/downloaded_packages')) unlink('/tmp/downloaded_packages', recursive = TRUE)" && \
# Remove examples directories from installed R packages to reduce image size
find $ROCK_LIB -type d -name "examples" -exec rm -rf {} + 2>/dev/null || true && \
# Set proper ownership
chown -R rock $ROCK_LIB