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

How to run the container with Docker:

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:

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).

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).

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'

#!/bin/bash

docker build  . -t lofarit/base3.10