- Fixed docker files for 1.13 support

Author: Alan Christie

Dockerfile-obabel

@@ -13,8 +13,6 @@ RUN apt-get update && apt-get install -y --no-install-recommends python-setuptoo
 # And the pip packages including pipeline-utilities and im-pipelines-utils-rdkit
 RUN pip install im-pipelines-utils==2.2.* im-pipelines-utils-rdkit==1.4.*
 
-USER obabel
-
 # The CMD is simply to run 'execute' in the WORKDIR.
 # The user would normally mount a volume with their own execute
 # script in it and then set the WORKDIR to the directory it's in.
@@ -25,7 +23,10 @@ USER obabel
 # which can be defined with the docker 'pipeline' build argument.
 ARG pipeline=informaticsmatters/pipelines-obabel:latest
 ENV PIPELINE=$pipeline
-WORKDIR /home/obable
-COPY --chown=obabel:0 execute ./
-RUN chmod +x ./execute
+WORKDIR /home/obabel
+COPY execute ./
+RUN chown obabel:0 ./execute && \
+    chmod +x ./execute
 CMD ["./execute"]
+
+USER obabel

Dockerfile-pli

@@ -11,7 +11,6 @@ WORKDIR /usr/local/pli
 RUN make
 
 RUN useradd -u 1001 -g 0 -m pli
-USER 1001
 
 WORKDIR /home/pli
 ENV PLI_DIR /usr/local/pli
@@ -26,6 +25,9 @@ ENV PLI_DIR /usr/local/pli
 # which can be defined with the docker 'pipeline' build argument.
 ARG pipeline=informaticsmatters/pli:latest
 ENV PIPELINE=$pipeline
-COPY --chown=1001:0 execute ./
-RUN chmod +x ./execute
+COPY execute ./
+RUN chown 1001:0 ./execute && \
+    chmod +x ./execute
 CMD ["./execute"]
+
+USER 1001

Dockerfile-smog

@@ -18,7 +18,6 @@ RUN wget https://sourceforge.net/projects/opengrowth/files/SMoG2016.tar.gz/downl
 ARG USERID=1001
 
 RUN useradd -u $USERID -g 0 -m smog
-USER $USERID
 
 # The CMD is simply to run 'execute' in the WORKDIR.
 # The user would normally mount a volume with their own execute
@@ -31,6 +30,9 @@ USER $USERID
 ARG pipeline=informaticsmatters/smog:latest
 ENV PIPELINE=$pipeline
 WORKDIR /home/smog
-COPY --chown=smog:0 execute ./
-RUN chmod +x ./execute
+COPY execute ./
+RUN chown $USERID:0 ./execute && \
+    chmod +x ./execute
 CMD ["./execute"]
+
+USER $USERID