Removed the run_pipelines.sh script. Changed and improved the README accordingly.

README.md

@@ -14,12 +14,16 @@ 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
 
-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).
 
 How to start prefactor3 once in the container:
 
-    $ ./run_pipelines.sh
+    $ genericpipeline.py Pre-Facet-Calibrator.parset -v -d -c pipeline.cfg
 
-This command will run the calibrator and target pipelines in sequence. Feel free to have a look and change the files as pipeline.cfg, Pre-Facet-Calibrator.parset, Pre-Facet-Target.parset and run_pipelines.sh itself in the /home/lofar directory inside the container to suit your needs.
+..or:
+
+    $ genericpipeline.py Pre-Facet-Target.parset -v -d -c pipeline.cfg
+
+Feel free to have a look and change the files as pipeline.cfg, Pre-Facet-Calibrator.parset and Pre-Facet-Target.parset in the /home/lofar directory inside the container to suit your needs.
 
 Remember that the contents of the container (excluding data on your external volumes as the input/output data directories) will be wiped when you exit the container.
\ No newline at end of file

prefactor3/Dockerfile

@@ -43,10 +43,9 @@ RUN cd /opt/prefactor && git pull && git checkout d4f18ff # V3.0 tag hash
 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 run_pipelines.sh /home/lofar/run_pipelines.sh
 COPY data/input_data /input_data
 COPY data/output_data /output_data
-RUN chmod 755 -R /home/lofar/run_pipelines.sh && chown lofar:lofar /home/lofar && chown -R lofar:lofar /input_data && chown -R lofar:lofar /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

prefactor3/run_pipelines.sh

-#!/bin/bash
-set -e
-genericpipeline.py /home/lofar/Pre-Facet-Calibrator.parset -v -d -c /home/lofar/pipeline.cfg
-genericpipeline.py /home/lofar/Pre-Facet-Calibrator.parset -v -d -c /home/lofar/pipeline.cfg
\ No newline at end of file