- Adjustments for issue #33

  Built-in execute command (a help command)
  User now has to specify WORKDIR or CMD to do real work

Author: Alan Christie

Dockerfile-obabel

@@ -15,3 +15,17 @@ 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.
+# In its absence we just run the built-in 'execute',
+# which is expected to echo some descriptive/helpful text.
+#
+# The default 'execute' relies on an ENV to name the pipeline it's in,
+# 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
+CMD ["./execute"]

Dockerfile-pli

@@ -15,3 +15,17 @@ USER 1001
 
 WORKDIR /home/pli
 ENV PLI_DIR /usr/local/pli
+
+# 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.
+# In its absence we just run the built-in 'execute',
+# which is expected to echo some descriptive/helpful text.
+#
+# The default 'execute' relies on an ENV to name the pipeline it's in,
+# 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
+CMD ["./execute"]

Dockerfile-rdkit

@@ -12,3 +12,18 @@ RUN pip install -e /opt/python
 # And the pip packages including pipeline-utilities and im-pipelines-utils-rdkit
 RUN pip install molvs standardiser matplotlib \
         im-pipelines-utils>=2.4.5 im-pipelines-utils-rdkit>=1.5.7
+
+# 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.
+# In its absence we just run the built-in 'execute',
+# which is expected to echo some descriptive/helpful text.
+#
+# The default 'execute' relies on an ENV to name the pipeline it's in,
+# which can be defined with the docker 'pipeline' build argument.
+ARG pipeline=informaticsmatters/rdkit_pipelines:latest
+ENV PIPELINE=$pipeline
+WORKDIR /home/rdkit
+COPY execute ./
+RUN chmod +x ./execute
+CMD ["./execute"]

Dockerfile-rdkit-centos

@@ -11,4 +11,19 @@ COPY src/python /opt/python
 RUN pip install -e /opt/python
 # And the pip packages including pipeline-utilities and im-pipelines-utils-rdkit
 # NOTE: matplotlib is missing
-RUN pip install molvs standardiser im-pipelines-utils==2.2.* im-pipelines-utils-rdkit==1.4.*
+RUN pip install molvs standardiser im-pipelines-utils>=2.4.5 im-pipelines-utils-rdkit>=1.5.7
+
+# 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.
+# In its absence we just run the built-in 'execute',
+# which is expected to echo some descriptive/helpful text.
+#
+# The default 'execute' relies on an ENV to name the pipeline it's in,
+# which can be defined with the docker 'pipeline' build argument.
+ARG pipeline=informaticsmatters/rdkit_pipelines:latest
+ENV PIPELINE=$pipeline
+WORKDIR /home/rdkit
+COPY execute ./
+RUN chmod +x ./execute
+CMD ["./execute"]

Dockerfile-smog

@@ -20,5 +20,17 @@ 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
+# script in it and then set the WORKDIR to the directory it's in.
+# In its absence we just run the built-in 'execute',
+# which is expected to echo some descriptive/helpful text.
+#
+# The default 'execute' relies on an ENV to name the pipeline it's in,
+# which can be defined with the docker 'pipeline' build argument.
+ARG pipeline=informaticsmatters/smog:latest
+ENV PIPELINE=$pipeline
 WORKDIR /home/smog
+COPY --chown=smog:0 execute ./
+RUN chmod +x ./execute
+CMD ["./execute"]

build.gradle

@@ -64,6 +64,7 @@ task buildPipelinesImage(type: DockerBuildImage) {
     dockerFile = file('Dockerfile-rdkit')
     inputDir = file('.')
     tag = "informaticsmatters/rdkit_${pipeline}:latest"
+    buildArgs = ['pipeline':"informaticsmatters/rdkit_${pipeline}:latest"]
 }
 
 task buildPliImage(type: DockerBuildImage) {
@@ -73,6 +74,7 @@ task buildPliImage(type: DockerBuildImage) {
     dockerFile = file('Dockerfile-pli')
     inputDir = file('.')
     tag = "informaticsmatters/pli:latest"
+    buildArgs = ['pipeline':"informaticsmatters/pli:latest"]
 }
 
 task buildSmogImage(type: DockerBuildImage) {
@@ -82,6 +84,7 @@ task buildSmogImage(type: DockerBuildImage) {
     dockerFile = file('Dockerfile-smog')
     inputDir = file('.')
     tag = "informaticsmatters/smog:latest"
+    buildArgs = ['pipeline':"informaticsmatters/smog:latest"]
 }
 
 task buildSdPosterImage(type: DockerBuildImage) {
@@ -99,6 +102,7 @@ task buildObabelImage(type: DockerBuildImage) {
     dockerFile = file('Dockerfile-obabel')
     inputDir = file('.')
     tag = "informaticsmatters/pipelines-obabel:latest"
+    buildArgs = ['pipeline':"informaticsmatters/pipelines-obabel:latest"]
 }
 
 task buildDockerImages() {

execute

@@ -0,0 +1,32 @@
+#!/usr/bin/bash
+
+echo
+echo "PIPELINES (RDKit)"
+echo "-----------------"
+echo "You have just run the built-in 'execute' command. Congratulations!"
+echo ""
+echo "In order to use this container productively you need to provide your own"
+echo "'execute' script or command and any corresponding data files."
+echo ""
+echo "You could mount a volume into this container that contains an executable"
+echo "file named 'execute', which contains the command you wish to run,"
+echo "and also include any additional data files. When you run the container,"
+echo "adjust the default container WORKDIR by using the docker '-w' option,"
+echo "specifying the mounted path of the volume as its value. As an example,"
+echo "if you've placed an 'execute' and its data in the current working"
+echo "directory you could run the container like this: -"
+echo ""
+echo "  $ docker run --rm \\"
+echo "      -v \$PWD:/squonk/work/docker \\"
+echo "      -w=\"/squonk/work/docker\" \\"
+echo "      $PIPELINE"
+echo ""
+echo "Alternatively you can run interactive commands by over-riding the"
+echo "built-in container 'CMD' (which is './execute'). To enter the"
+echo "container's shell (bash) using the default 'WORKDIR' you can run: -"
+echo ""
+echo "  $ docker run --rm \\"
+echo "      -it \\"
+echo "      $PIPELINE \\"
+echo "      bash"
+echo