Browse code

Dockerfile updates.

Markus Riester authored on 10/12/2023 21:42:36
Showing 1 changed files

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@@ -1,5 +1,5 @@
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-#FROM bioconductor/bioconductor_docker:RELEASE_3_17
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-FROM bioconductor/bioconductor_docker:devel
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+FROM bioconductor/bioconductor_docker:RELEASE_3_18
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+#FROM bioconductor/bioconductor_docker:devel
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 # install base packages
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 RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}; \
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@@ -33,13 +33,13 @@ RUN apt update \
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 # install GenomicsDB
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 ENV GENOMICSDB_PATH=/opt/GenomicsDB
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-ENV GENOMICSDB_BRANCH=develop
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+ENV GENOMICSDB_BRANCH=master
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 RUN mkdir $GENOMICSDB_PATH
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 ENV INSTALL_PREFIX=$GENOMICSDB_PATH
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 ENV PREREQS_ENV=$GENOMICSDB_PATH/genomicsdb_prereqs.sh
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 ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64
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-ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-arm64
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-ENV MAVEN_VERSION=3.9.3
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+#ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-arm64
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+ENV MAVEN_VERSION=3.9.5
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 RUN ls $JAVA_HOME
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@@ -59,11 +59,11 @@ RUN chmod +x $PREREQS_ENV && \
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 # install GenomicsDB R bindings
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 RUN Rscript -e 'library(remotes);\
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-remotes::install_github("nalinigans/GenomicsDB-R", ref="develop", configure.args="--with-genomicsdb=/opt/GenomicsDB/")'
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+remotes::install_github("nalinigans/GenomicsDB-R", ref="master", configure.args="--with-genomicsdb=/opt/GenomicsDB/")'
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 # install PureCN
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-#RUN Rscript -e 'BiocManager::install("PureCN", dependencies = TRUE)'
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-RUN Rscript -e 'BiocManager::install("lima1/PureCN", ref = "RELEASE_3_17", dependencies = TRUE)'
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+RUN Rscript -e 'BiocManager::install("PureCN", dependencies = TRUE)'
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+#RUN Rscript -e 'BiocManager::install("lima1/PureCN", ref = "RELEASE_3_18", dependencies = TRUE)'
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 ENV PURECN=/usr/local/lib/R/site-library/PureCN/extdata
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 # add symbolic link and paths