Decoupled base and prefactor code into two separate containers and moved to...

Decoupled base and prefactor code into two separate containers and moved to new container names nomenclature.

README.md

@@ -8,11 +8,11 @@ This container is based on the "lofaruser/imaging-pipeline:v3.10" base image, an
 
 How to run the container with Docker:
 
-    docker run --rm -v $INPUT_DATA_FOLDER:/input_data,$OUTPUT_DATA_FOLDER:/output_data -it lofarit/prefactor3:pipeline_v3.10
+    docker run --rm -v $INPUT_DATA_FOLDER:/input_data,$OUTPUT_DATA_FOLDER:/output_data -it lofarit/lofarit/prefactor3_base3.10
     
 How to run the container wth Singularity:
 
-    singularity run --pid --writable-tmpfs --containall --cleanenv -B$INPUT_DATA_FOLDER:/input_data,$OUTPUT_DATA_FOLDER:/output_data docker://lofarit/prefactor3:pipeline_v3.10
+    singularity run --pid --writable-tmpfs --containall --cleanenv -B$INPUT_DATA_FOLDER:/input_data,$OUTPUT_DATA_FOLDER:/output_data docker://lofarit lofarit/prefactor3_base3.10
 
 These commands will start the container and place you in the /home/lofar directlry inside the container. In both cases you have to set the $INPUT_DATA_FOLDER and $OUTPUT_DATA_FOLDER to the input and output data folders respectively, on the host system (i.e. the machine on which you are running the container). Note that the output data folder must exists and have write permissions (if using Singularty, by the user running the container).
 

base/Dockerfile

+FROM lofaruser/imaging-pipeline:v3.10
+
+# 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='base3.10'

base/build_docker_container.sh

+#!/bin/bash
+
+docker build  . -t lofarit/base3.10

prefactor3/entrypoint.sh → base/entrypoint.sh

@@ -14,14 +14,14 @@ echo "[INFO] Creating /tmp/lofarhome to be used as lofar home"
 mkdir /tmp/lofarhome
 
 echo "[INFO] Initialising /tmp/lofarhome with configuration files"
-cp -a /home/vanilla_lofar/* /tmp/lofarhome
+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 @prefactor3 container"
-echo 'export PS1="${debian_chroot:+($debian_chroot)}\u@prefactor3@\h:\w\$ "' > /tmp/lofarhome/.bashrc
+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
@@ -37,7 +37,9 @@ echo -n "[INFO] Will execute entrypoint command: "
 echo $COMMAND
 echo ""
 echo "=============================================================="
-echo "|             Welcome to the Prefactor3 container!           |"
+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)\"."

base/run_docker_container.sh

+#!/bin/bash
+docker run --rm -v $PWD/data:/data -it lofarit/base3.10 /bin/bash

prefactor3/Dockerfile

-FROM lofaruser/imaging-pipeline:v3.10
-
-# 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
-
+FROM lofarit/base3.10
 
 #------------------------
 # Get prefactor
 #------------------------
-
+USER root
 RUN cd /opt && git clone https://github.com/lofar-astron/prefactor
 RUN cd /opt/prefactor && git pull && git checkout d4f18ff # V3.0 tag hash
+USER lofar
 
 # Add conf and run scripts
-COPY pipeline.cfg /home/lofar/pipeline.cfg
-COPY Pre-Facet-Calibrator.parset /home/lofar/Pre-Facet-Calibrator.parset
-COPY Pre-Facet-Target.parset /home/lofar/Pre-Facet-Target.parset
-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
+COPY pipeline.cfg /home/vanilla_lofar/pipeline.cfg
+COPY Pre-Facet-Calibrator.parset /home/vanilla_lofar/Pre-Facet-Calibrator.parset
+COPY Pre-Facet-Target.parset /home/vanilla_lofar/Pre-Facet-Target.parset
 
-
-#----------------------
-# Entrypoint
-#----------------------
-
-# Copy entrypoint
-COPY entrypoint.sh /
-
-# Give right permissions
-RUN chmod 755 /entrypoint.sh
-
-# Set entrypoint
-ENTRYPOINT ["/entrypoint.sh"]
-
-# Set user lofar
-USER lofar
+ENV CONTAINER_NAME='prefactor3_base3.10'

prefactor3/build_docker_container.sh

 #!/bin/bash
 
-docker build  . -t lofarit/prefactor3:pipeline_v3.10
+docker build  . -t lofarit/prefactor3_base3.10

prefactor3/run_docker_container.sh

 #!/bin/bash
-docker run --rm -v $PWD/data:/data -it lofarit/prefactor3:pipeline_v3.10 /bin/bash
+docker run --rm -v $PWD/data:/data -it lofarit/prefactor3_base3.10 /bin/bash

prefactor3/run_singularity_container.sh

 #!/bin/bash
-singularity run --pid --writable-tmpfs --containall --cleanenv -Bdata/lofar/input_data:/data/lofar/input_data,data/lofar/output_data:/data/lofar/output_data docker://lofarit/prefactor3
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+singularity run --pid --writable-tmpfs --containall --cleanenv -Bdata/lofar/input_data:/data/lofar/input_data,data/lofar/output_data:/data/lofar/output_data docker://lofarit/prefactor3_base3.10
\ No newline at end of file