From d0dcc83a86665be44e3075dcce38a6528efae140 Mon Sep 17 00:00:00 2001 From: Markus Riester Date: Sun, 10 Dec 2023 16:42:36 -0500 Subject: [PATCH] Dockerfile updates. --- Dockerfile | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/Dockerfile b/Dockerfile index 5985435..f55f640 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ -#FROM bioconductor/bioconductor_docker:RELEASE_3_17 -FROM bioconductor/bioconductor_docker:devel +FROM bioconductor/bioconductor_docker:RELEASE_3_18 +#FROM bioconductor/bioconductor_docker:devel # install base packages RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)){install.packages("BiocManager")}; \ @@ -33,13 +33,13 @@ RUN apt update \ # install GenomicsDB ENV GENOMICSDB_PATH=/opt/GenomicsDB -ENV GENOMICSDB_BRANCH=develop +ENV GENOMICSDB_BRANCH=master RUN mkdir $GENOMICSDB_PATH ENV INSTALL_PREFIX=$GENOMICSDB_PATH ENV PREREQS_ENV=$GENOMICSDB_PATH/genomicsdb_prereqs.sh ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64 -ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-arm64 -ENV MAVEN_VERSION=3.9.3 +#ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-arm64 +ENV MAVEN_VERSION=3.9.5 RUN ls $JAVA_HOME @@ -59,11 +59,11 @@ RUN chmod +x $PREREQS_ENV && \ # install GenomicsDB R bindings RUN Rscript -e 'library(remotes);\ -remotes::install_github("nalinigans/GenomicsDB-R", ref="develop", configure.args="--with-genomicsdb=/opt/GenomicsDB/")' +remotes::install_github("nalinigans/GenomicsDB-R", ref="master", configure.args="--with-genomicsdb=/opt/GenomicsDB/")' # install PureCN -#RUN Rscript -e 'BiocManager::install("PureCN", dependencies = TRUE)' -RUN Rscript -e 'BiocManager::install("lima1/PureCN", ref = "RELEASE_3_17", dependencies = TRUE)' +RUN Rscript -e 'BiocManager::install("PureCN", dependencies = TRUE)' +#RUN Rscript -e 'BiocManager::install("lima1/PureCN", ref = "RELEASE_3_18", dependencies = TRUE)' ENV PURECN=/usr/local/lib/R/site-library/PureCN/extdata # add symbolic link and paths