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@@ -1,4 +1,4 @@
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-#FROM bioconductor/bioconductor_docker:RELEASE_3_15
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+#FROM bioconductor/bioconductor_docker:RELEASE_3_17
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FROM bioconductor/bioconductor_docker:devel
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# install base packages
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@@ -12,49 +12,58 @@ RUN Rscript -e 'BiocManager::install(c("GenomicRanges", "IRanges", "DNAcopy", "B
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# patched PSCBS with support of interval weights
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RUN Rscript -e 'BiocManager::install("lima1/PSCBS", ref="add_dnacopy_weighting")'
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-RUN apt-get update \
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- && apt-get install -y --no-install-recommends apt-utils python-is-python3 \
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+RUN apt update \
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+ && apt install -y --no-install-recommends apt-utils python-is-python3 \
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+ openjdk-17-jre-headless \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/*
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-RUN apt-get install -y --no-install-recommends \
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- texlive \
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- texlive-latex-extra \
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- texlive-fonts-extra \
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- texlive-bibtex-extra \
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- texlive-science \
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- texi2html \
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- texinfo \
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- && apt-get clean \
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- && rm -rf /var/lib/apt/lists/*
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+# tex support for building vignettes
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+# RUN apt update \
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+# && apt install -y --no-install-recommends \
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+# texlive \
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+# texlive-latex-extra \
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+# texlive-fonts-extra \
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+# texlive-bibtex-extra \
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+# texlive-science \
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+# texi2html \
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+# texinfo \
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+# && apt-get clean \
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+# && rm -rf /var/lib/apt/lists/*
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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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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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+
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+RUN ls $JAVA_HOME
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WORKDIR /tmp
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-RUN git clone -b develop https://github.com/GenomicsDB/GenomicsDB && \
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- cd GenomicsDB && \
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- git checkout f945f3db507c32e460033c284addc801a05b6919
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-RUN cd GenomicsDB/scripts/prereqs && \
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+
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+RUN git clone --recursive --branch $GENOMICSDB_BRANCH https://github.com/GenomicsDB/GenomicsDB.git && \
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+ cd GenomicsDB/scripts/prereqs && \
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./install_prereqs.sh && \
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apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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-RUN chmod +x $GENOMICSDB_PATH/genomicsdb_prereqs.sh && \
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- $GENOMICSDB_PATH/genomicsdb_prereqs.sh && \
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- cmake -DCMAKE_INSTALL_PREFIX=$GENOMICSDB_PATH ./GenomicsDB && \
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+
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+RUN chmod +x $PREREQS_ENV && \
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+ $PREREQS_ENV && \
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+ cmake -DCMAKE_INSTALL_PREFIX=$GENOMICSDB_PATH -DCMAKE_BUILD_TYPE=Release ./GenomicsDB && \
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make && make install && \
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rm -rf /tmp/GenomicsDB
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-
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+
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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="master", configure.args="--with-genomicsdb=/opt/GenomicsDB/")'
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+remotes::install_github("nalinigans/GenomicsDB-R", ref="develop", 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", dependencies = TRUE)'
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+RUN Rscript -e 'BiocManager::install("lima1/PureCN", ref = "RELEASE_3_17", 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
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...
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@@ -63,7 +72,7 @@ WORKDIR /opt
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RUN ln -s $PURECN /opt/PureCN
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# install GATK4
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-ENV GATK_VERSION="4.2.6.1"
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+ENV GATK_VERSION="4.4.0.0"
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RUN wget --no-verbose https://github.com/broadinstitute/gatk/releases/download/${GATK_VERSION}/gatk-${GATK_VERSION}.zip && \
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unzip gatk-${GATK_VERSION}.zip -d /opt && \
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rm gatk-${GATK_VERSION}.zip
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