Docker changes

Docker/Dockerfile-base

@@ -181,7 +181,7 @@ LABEL \
     nl.astron.linc.dp3.version=${DP3_VERSION} \
     nl.astron.linc.wsclean.version=${WSCLEAN_VERSION}
 
-# Only install run-time required packages
+# Only install run-time required packages 
 RUN export DEBIAN_FRONTEND=noninteractive && \
     apt-get update && \
     apt-get install -y \

docs/source/running.rst

@@ -66,13 +66,13 @@ For Docker::
 
 To run **LINC** you only need to add the container-specific execution command and **make sure that all necessary volumes are mounted read-write** (``<mount_points>``) and are thus accessible from inside the container, e.g.,::
 
-    $ singularity exec --bind <mount_points>:<mount_points> <linc.sif> cwltool --no-container <cwl_options> /usr/local/share/linc/workflows/HBA_calibrator.cwl LINC.json
+    $ singularity exec --bind <mount_points>:<mount_points> <linc.sif> cwltool --no-container --preserve-entire-environment <cwl_options> /usr/local/share/linc/workflows/HBA_calibrator.cwl LINC.json
 
 where ``<linc.sif>`` is the location of the Singularity image, or ::
 
-    $ docker run --rm <docker_options> -v <mount_points>:<mount_points> -w $PWD astronrd/linc cwltool --no-container <cwl_options> /usr/local/share/linc/workflows/HBA_calibrator.cwl LINC.json
+    $ docker run --rm <docker_options> -v <mount_points>:<mount_points> -w $PWD astronrd/linc cwltool --no-container --preserve-entire-environment <cwl_options> /usr/local/share/linc/workflows/HBA_calibrator.cwl LINC.json
 
-Since you are running **LINC** inside a container, do not forget to add the ``--no-container`` flag to your call, no matter whether you use Singularity or Docker. Do **not** use the ``--singularity`` flag.
+Since you are running **LINC** inside a container, do not forget to add the ``--no-container`` and ``--preserve-entire-environment`` flag to your call, no matter whether you use Singularity or Docker. Do **not** use the ``--singularity`` flag.
 
 Pipeline options for ``cwltool``
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