Merge branch 'devel' of https://github.com/lima1/PureCN into devel

Dockerfile

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