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Automate the previously needed manual startup steps #13

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34495a9
Automate the previously needed manual startup steps
davidspek Oct 26, 2020
2f98e5e
Fix wrong rserve.conf dir
davidspek Oct 26, 2020
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9 changes: 6 additions & 3 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ RUN apt-get update && \
littler \
r-base \
r-base-dev \
r-recommended && \
r-recommended && \
ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r && \
ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r && \
install.r docopt && \
Expand All @@ -73,8 +73,10 @@ RUN install2.r RColorBrewer xtable fitdistrplus som ROCR RJSONIO gplots e1071 ca
# Install all R packages from Bioconductor
RUN R -e 'BiocManager::install(c("impute", "pcaMethods", "siggenes", "globaltest", "GlobalAncova", "Rgraphviz", "KEGGgraph", "preprocessCore", "genefilter", "SSPA", "sva", "limma", "mzID", "xcms"))'

ADD rserve.conf /rserve.conf
ADD rserve.conf /etc/rserve.conf
ADD metab4script.R /metab4script.R
ADD run.sh /run.sh
RUN chmod +x /run.sh

# Download and Install Payara Micro
# From payara/micro github - https://github.com/payara/docker-payaramicro/blob/master/Dockerfile
Expand Down Expand Up @@ -106,4 +108,5 @@ ENV METABOANALYST_FILE_NAME MetaboAnalyst.war

RUN wget --quiet -O $DEPLOY_DIR/$METABOANALYST_FILE_NAME $METABOANALYST_LINK

ENTRYPOINT ["bin/bash"]
ENTRYPOINT ["java", "-XX:+UseContainerSupport", "-XX:MaxRAMPercentage=90.0", "-jar", "/opt/payara/payara-micro.jar"]
CMD ["/run.sh", "--deploymentDir", "/opt/payara/deployments"]
2 changes: 2 additions & 0 deletions run.sh
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@@ -0,0 +1,2 @@
#!/usr/bin/env bash
Rscript /metab4script.R > /dev/null 2>&1