Add containerized Vizapp

Containerize the Vizapp

vizapp/src/Dockerfile

+FROM git.biohpc.swmed.edu:5050/astrocyte/container/r:4.2.2
+
+# Install dependencies for building R packages
+RUN mkdir -p /astrocyte /apps /home1 /home2 /work /project /archive /cm /programs && \
+    yum -y update && \
+    yum install -y wget \
+     && \
+    yum clean all
+    #yum install -y glpk-devel \
+
+# Update gcc to gcc 7
+RUN yum install -y centos-release-scl && \
+    yum install -y devtoolset-7 && \
+    yum clean all 
+
+# Update glpk, required by igraph 2 and above
+RUN source scl_source enable devtoolset-7 && \
+    wget -q ftp://ftp.gnu.org/gnu/glpk/glpk-4.65.tar.gz && \
+    tar -xzf glpk-4.65.tar.gz && \
+    cd glpk-4.65 && \
+    ./configure  && \
+    make -j8 && \
+    make check && \
+    make install && \
+    ldconfig --verbose && \
+    make clean  && \
+    cd .. && \
+    rm -fr glpk-4.65
+
+ # Install R packages
+RUN source scl_source enable devtoolset-7 && \
+    /usr/local/bin/R -e "install.packages('https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/RcppArmadillo_0.12.6.1.0.tar.gz', repos=NULL, type='source')"
+
+# Update cpp11, required by igraph 2
+RUN source scl_source enable devtoolset-7 && \
+    /usr/local/bin/R -e "install.packages('https://cran.r-project.org/src/contrib/cpp11_0.4.7.tar.gz', repos=NULL, type='source')"
+
+RUN source scl_source enable devtoolset-7 && \
+    /usr/local/bin/R -e "install.packages('https://cran.r-project.org/src/contrib/igraph_2.0.2.tar.gz', repos=NULL, type='source')"
+
+RUN source scl_source enable devtoolset-7 && \
+    /usr/local/bin/R -e "install.packages(c('ggplot2'), repos='https://cloud.r-project.org')"
+
+# Install latest version of ggtree
+RUN source scl_source enable devtoolset-7 && \
+    /usr/local/bin/R -e  "devtools::install_github('YuLab-SMU/ggtree', quietly=TRUE, upgrade_dependencies=TRUE)"
+
+# Install Bioconductor packages
+RUN source scl_source enable devtoolset-7 && \
+    /usr/local/bin/R -e "BiocManager::install('ChIPseeker',quietly=TRUE, update=FALSE)"
+
+RUN source scl_source enable devtoolset-7 && \
+    /usr/local/bin/R -e "BiocManager::install('org.Hs.eg.db', quietly=TRUE, update=FALSE)"
+
+RUN mkdir -p /vizapp
+COPY ui.R server.R /vizapp
+
+ARG VIZAPP_PORT=8123
+ENV VIZAPP_PORT=$VIZAPP_PORT
+
+# Default command
+CMD ["/usr/local/bin/R", "-e", "shiny::runApp('/vizapp', port=as.numeric(Sys.getenv('VIZAPP_PORT')))"]