From 7905ce83fe0975f5cc421a7be3353545879a00eb Mon Sep 17 00:00:00 2001 From: Markus Riester Date: Sun, 12 May 2024 10:02:49 -0400 Subject: [PATCH] Updated Dockerfile --- Dockerfile | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/Dockerfile b/Dockerfile index f55f640..1b5114d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM bioconductor/bioconductor_docker:RELEASE_3_18 +FROM bioconductor/bioconductor_docker:RELEASE_3_19 #FROM bioconductor/bioconductor_docker:devel # install base packages @@ -37,11 +37,9 @@ 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=3.9.5 - -RUN ls $JAVA_HOME +#ARG TARGETPLATFORM +#RUN if [ "$TARGETPLATFORM" = "linux/amd64" ]; then JAVA_HOME="/usr/lib/jvm/java-17-openjdk-amd64"; else JAVA_HOME=/usr/lib/jvm/java-17-openjdk-arm64; fi +#ENV MAVEN_VERSION=3.9.5 WORKDIR /tmp @@ -63,7 +61,7 @@ remotes::install_github("nalinigans/GenomicsDB-R", ref="master", configure.args= # install PureCN RUN Rscript -e 'BiocManager::install("PureCN", dependencies = TRUE)' -#RUN Rscript -e 'BiocManager::install("lima1/PureCN", ref = "RELEASE_3_18", dependencies = TRUE)' +#RUN Rscript -e 'BiocManager::install("lima1/PureCN", ref = "RELEASE_3_19", dependencies = TRUE)' ENV PURECN=/usr/local/lib/R/site-library/PureCN/extdata # add symbolic link and paths @@ -72,7 +70,7 @@ WORKDIR /opt RUN ln -s $PURECN /opt/PureCN # install GATK4 -ENV GATK_VERSION="4.4.0.0" +ENV GATK_VERSION="4.5.0.0" RUN wget --no-verbose https://github.com/broadinstitute/gatk/releases/download/${GATK_VERSION}/gatk-${GATK_VERSION}.zip && \ unzip gatk-${GATK_VERSION}.zip -d /opt && \ rm gatk-${GATK_VERSION}.zip