dockerfile-gh-varseq

ARG BASE_IMAGE="registry.goldenhelix.com/public/ghdesktop-office-web:latest"
FROM $BASE_IMAGE AS base_layer

USER root

ENV STARTUPDIR /dockerstartup
ENV INST_SCRIPTS $STARTUPDIR/install
WORKDIR $HOME

######### Customize Container Here ###########

ARG VS_VERSION=2.6.2

# URL to download the VarSeq installer
ARG DOWNLOAD_BASE_URL="http://proxy.goldenhelix.com:8080/Installers/"
#ARG DOWNLOAD_BASE_URL="http://proxy.goldenhelix.com:8080/Nightly/"
#ARG DOWNLOAD_BASE_URL="https://www.goldenhelix.com/Downloads/VarSeq/"
# Optional
ARG DOWNLOAD_FILE_SUFFIX="--SP1"
ARG DOWNLOAD_FILE_PREFIX=""

COPY  ./src/gh/install/vs_custom_startup.sh $STARTUPDIR/custom_startup.sh
COPY ./src/gh/install/install_varseq.sh $INST_SCRIPTS/varseq/
RUN bash $INST_SCRIPTS/varseq/install_varseq.sh "${DOWNLOAD_BASE_URL}/${DOWNLOAD_FILE_PREFIX}VarSeq-Lin64-${VS_VERSION}${DOWNLOAD_FILE_SUFFIX}.tar.gz" \
  && rm -rf $INST_SCRIPTS/varseq/ \
  && chmod +x $STARTUPDIR/custom_startup.sh \
  && chmod 755 $STARTUPDIR/custom_startup.sh

# Clear this if you don't want to shutdown the container if VarSeq exists
ENV MONITOR_PROCESS 1

# This is only needed for VarSeq 2, it fixes xdg-open being called with quoted files
COPY ./src/gh/install/xdg-open /usr/local/bin/xdg-open
# Set as executable or delete it based on the INSTALL_XDG_OPEN flag
ARG INSTALL_XDG_OPEN=false
RUN if [ "$INSTALL_XDG_OPEN" = "true" ]; then \
      chmod +x /usr/local/bin/xdg-open; \
    else \
      rm /usr/local/bin/xdg-open; \
    fi

# Add to task bar (each of these launcher-5 numbers is a slot in the app launcher)
RUN cp /usr/share/applications/varseq.desktop .config/xfce4/panel/launcher-5/17306804705.desktop

######### End Customizations ###########

RUN chown 1000:0 $HOME

ENV HOME /home/ghuser
WORKDIR $HOME
RUN mkdir -p $HOME && chown -R 1000:0 $HOME

USER 1000