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Dockerfile Update #47

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Dockerfile Update #47

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8fe3421
adding GAMBLR.utils to Dockerfile, necessary for users running DLBCLo…
lklossok Mar 19, 2026
3ca6fc1
add optparse
lklossok Mar 19, 2026
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15 changes: 8 additions & 7 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ LABEL description="Docker container for GAMBLR.predict (pinned & low-RAM build)"
ARG GAMBLR_DATA_REF=v1.3.1
ARG GAMBLR_HELPERS_REF=v1.3.1
ARG GAMBLR_PREDICT_REF=v1.2
ARG GAMBLR_UTILS_REF=v1.3

# ---- Keep RAM use low during installs ----
ENV PAK_NUM_WORKERS=1 \
Expand All @@ -31,13 +32,13 @@ RUN R -q -e "install.packages('BiocManager', repos='${CRAN_MIRROR}')"

# ---- CRAN packages ----
RUN R -q -e "pak::pkg_install(c( \
'caret','circlize','dplyr','DT','FNN','ggalluvial','ggrepel','ggside', \
'grid','mclust','purrr','randomForest','readr','shinybusy','shinyjs', \
'tibble','tidyr','tidyselect','plotly','ggpubr','readxl','uwot' \
'optparse','data.table','caret','circlize','dplyr','DT','FNN','ggalluvial','ggrepel','ggside', \
'grid','methods','mclust','purrr','randomForest','readr','rtracklayer','shinybusy','shinyjs', \
'stringr','S4Vectors','tibble','tidyr','tidyselect','plotly','ggpubr','ggplot2','readxl','uwot' \
), ask = FALSE)"

# ---- Bioconductor packages (from Bioc, not GitHub) ----
RUN R -q -e "BiocManager::install(c('IRanges','ComplexHeatmap'), ask=FALSE, update=FALSE)"
RUN R -q -e "BiocManager::install(c('IRanges','ComplexHeatmap','GenomicDistributions','GenomicRanges'), ask=FALSE, update=FALSE)"

# Install remotes (small, fast), then install GAMBLR.data with low-memory flags
RUN R -q -e "install.packages('remotes', repos='https://cran.r-project.org')"
Expand All @@ -55,19 +56,19 @@ RUN R -q -e " \

RUN R -q -e "pak::pkg_install(sprintf('morinlab/GAMBLR.helpers@%s', Sys.getenv('GAMBLR_HELPERS_REF', '${GAMBLR_HELPERS_REF}')), ask=FALSE)"
RUN R -q -e "pak::pkg_install(sprintf('morinlab/GAMBLR.predict@%s', Sys.getenv('GAMBLR_PREDICT_REF', '${GAMBLR_PREDICT_REF}')), ask=FALSE)"
RUN R -q -e "pak::pkg_install(sprintf('morinlab/GAMBLR.utils@%s', Sys.getenv('GAMBLR_UTILS_REF', '${GAMBLR_UTILS_REF}')), ask=FALSE)"

# ---- Smoke tests: fail early if anything is missing ----
RUN R -q -e " \
stopifnot(requireNamespace('GAMBLR.data', quietly=TRUE)); \
stopifnot(requireNamespace('GAMBLR.helpers', quietly=TRUE)); \
stopifnot(requireNamespace('GAMBLR.predict', quietly=TRUE)); \
stopifnot(requireNamespace('GAMBLR.utils', quietly=TRUE)); \
cat('Installed versions:\\n'); \
for(p in c('GAMBLR.data','GAMBLR.helpers','GAMBLR.predict')) \
for(p in c('GAMBLR.data','GAMBLR.helpers','GAMBLR.predict','GAMBLR.utils')) \
cat(' ', p, as.character(packageVersion(p)), '\\n') \
"
RUN R -q -e "pak::pkg_install('jlmelville/uwot@v0.2.3', ask=FALSE)"
EXPOSE 8787 3838

HEALTHCHECK CMD R -q -e "cat('ok')" || exit 1