From 87ec85e3867262e7f0bb0b6c68cdc0a6cceb7575 Mon Sep 17 00:00:00 2001
From: Stefano Alberto Russo <stefano.russo@gmail.com>
Date: Thu, 26 Mar 2020 16:14:34 +0100
Subject: [PATCH] Removed the run_pipelines.sh script. Changed and improved the
README accordingly.
---
README.md | 10 +++++++---
prefactor3/Dockerfile | 3 +--
prefactor3/run_pipelines.sh | 4 ----
3 files changed, 8 insertions(+), 9 deletions(-)
delete mode 100755 prefactor3/run_pipelines.sh
diff --git a/README.md b/README.md
index eca4887..59e2597 100644
--- a/README.md
+++ b/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
diff --git a/prefactor3/Dockerfile b/prefactor3/Dockerfile
index 1fc9d50..198051e 100644
--- a/prefactor3/Dockerfile
+++ b/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
diff --git a/prefactor3/run_pipelines.sh b/prefactor3/run_pipelines.sh
deleted file mode 100755
index e9c281d..0000000
--- a/prefactor3/run_pipelines.sh
+++ /dev/null
@@ -1,4 +0,0 @@
-#!/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
--
GitLab