Merge branch 'feature/base_v4' into develop

base_v4/Dockerfile

+FROM lofar/lofar-pipeline:LOFAR-Release-4_0_16
+
+# Set non-interactive
+ENV DEBIAN_FRONTEND noninteractive
+
+# Always update when extending base images
+RUN apt update
+
+
+#------------------------
+# Install deps
+#------------------------
+
+# Git, Curl, sudo and  Nano
+RUN apt-get install git curl sudo nano -y
+
+
+#------------------------
+# Lofar user
+#------------------------
+
+# Add group. We chose GID 65527 to try avoiding conflicts.
+RUN groupadd -g 65527 lofar
+
+# Add user. We chose UID 65527 to try avoiding conflicts.
+RUN useradd lofar -d /home/lofar -u 65527 -g 65527 -m -s /bin/bash
+
+# Add metuaser user to sudoers
+RUN adduser lofar sudo
+
+# No pass sudo (for everyone, actually)
+COPY sudoers /etc/sudoers
+
+# Setup home and input/output data directories
+COPY data/input_data /input_data
+COPY data/output_data /output_data
+RUN chown lofar:lofar /home/lofar && chown -R lofar:lofar /input_data && chown -R lofar:lofar /output_data
+
+# This is required mainly for Singularity
+RUN mv /home/lofar /home/vanilla_lofar
+RUN ln -s /tmp/lofarhome /home/lofar
+RUN rm -rf /tmp/lofarhome
+
+
+#----------------------
+# Entrypoint
+#----------------------
+
+# Copy entrypoint
+COPY entrypoint.sh /
+
+# Give right permissions
+RUN chmod 755 /entrypoint.sh
+
+# Set entrypoint
+ENTRYPOINT ["/entrypoint.sh"]
+
+# Set user lofar
+USER lofar
+
+# Set container name
+ENV CONTAINER_NAME='base4.0.16'

base_v4/build_docker_container.sh

+#!/bin/bash
+
+docker build  . -t lofarit/base4.0.16

base_v4/data/input_data/README.md

+Put here "calib" and "target" MS data (or link agains a folder containing them).

base_v4/data/output_data/README.md

+Directory for output data.

base_v4/entrypoint.sh

+#!/bin/bash
+
+# Exit on any error. More complex thing could be done in future
+# (see https://stackoverflow.com/questions/4381618/exit-a-script-on-error)
+set -e
+
+echo ""
+echo "[INFO] Executing entrypoint..."
+
+#echo "[INFO] Sourcing env in /opt/lofarsoft/lofarinit.sh..."
+#source /opt/lofarsoft/lofarinit.sh
+
+echo "[INFO] Creating /tmp/lofarhome to be used as lofar home"
+mkdir /tmp/lofarhome
+
+echo "[INFO] Initialising /tmp/lofarhome with configuration files"
+cp -aT /home/vanilla_lofar /tmp/lofarhome
+
+echo "[INFO] Moving to /home/lofar and setting as home"
+cd /home/lofar
+export HOME=/home/lofar
+
+echo "[INFO] Setting new prompt @$CONTAINER_NAME container"
+echo 'export PS1="${debian_chroot:+($debian_chroot)}\u@$CONTAINER_NAME@\h:\w\$ "' >> /tmp/lofarhome/.bashrc
+
+# Set entrypoint command
+if [ "x$@" == "x" ]; then
+    COMMAND="/bin/bash"
+else
+    COMMAND="$@"
+fi
+
+
+
+# Start!
+echo -n "[INFO] Will execute entrypoint command: "
+echo $COMMAND
+echo ""
+echo "=============================================================="
+echo ""
+echo "      Welcome to the LOFAR-IT $CONTAINER_NAME container!"
+echo ""
+echo "=============================================================="
+echo ""
+echo "You are now in /home/lofar with write access as user \"$(whoami)\"."
+echo ""
+echo "Remember that contents inside this container, unless stored"
+echo "on a persistent volume mounted from you host machine, will"
+echo "be wiped out when exiting the container."
+echo ""
+
+exec $COMMAND
+

base_v4/run_docker_container.sh

+#!/bin/bash
+docker run --rm -v $PWD/data:/data -it lofarit/base4.0.16 /bin/bash

base_v4/sudoers

+#
+# This file MUST be edited with the 'visudo' command as root.
+#
+# Please consider adding local content in /etc/sudoers.d/ instead of
+# directly modifying this file.
+#
+# See the man page for details on how to write a sudoers file.
+#
+Defaults        env_reset
+Defaults        mail_badpass
+Defaults        secure_path="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
+
+# Host alias specification
+
+# User alias specification
+
+# Cmnd alias specification
+
+# User privilege specification
+root    ALL=(ALL:ALL) ALL
+
+# Members of the admin group may gain root privileges
+%admin ALL=(ALL) ALL
+
+# Allow members of group sudo to execute any command
+%sudo   ALL=(ALL:ALL) NOPASSWD:ALL
+
+# See sudoers(5) for more information on "#include" directives:
+
+#includedir /etc/sudoers.d