Adding Dockerfile for module specific Docker image

bahill · bahill · commit 2baf2e51164e · 2021-05-17T15:28:04.000-04:00
diff --git a/Dockerfile b/Dockerfile
@@ -0,0 +1,23 @@
+### copyright 2017-2021 Regents of the University of California and the Broad Institute. All rights reserved.
+FROM genepattern/docker-python36:0.4
+
+MAINTAINER Barbara Hill <bhill@broadinstitute.org>
+
+# While you are debugging/iterating over your module code in the Module integrator comment out the secion below.
+# When you are done, export your module, unzip and move your source files into the src directory in this local workspace.
+# Then, update this section for you module and build using the docker build command below - again updated for your module.
+# -----------------------------------
+RUN mkdir /ExampleModule \
+    && chown gpuser /ExampleModule
+
+USER gpuser
+COPY src/*.py /ExampleModule/
+
+RUN /ExampleModule/ExampleModule.py
+# -----------------------------------
+
+# docker build --rm https://github.com/genepattern/ExampleModule#develop -f Dockerfile -t genepattern/example-module:2
+# make sure this repo and tag match the manifest & don't forget to docker push!
+
+# you can use this command to run Docker and iterate locally (update for your paths and module name, of course)
+# docker run --rm -it --user gpuser -v /c/Users/MyUSER/PathTo/ExampleModule:/mnt/mydata:rw genepattern/example-module:<tag> bash
diff --git a/manifest b/manifest
@@ -4,8 +4,11 @@ JVMLevel=
 LSID=urn\:lsid\:broad.mit.edu\:cancer.software.genepattern.module.analysis\:00374\:2.0
 author=Edwin F. Juarez;UCSD - Mesirov Lab
 categories=administration
-commandLine=<python_3.6> <libdir>ExampleModule.py -f <filename> -a <add_custom_message> -m <message_to_add> -o <output_filename>
-job.docker.image=genepattern/docker-python36:0.4
+#commandLine when run with source in Docker container:
+commandLine=/ExampleModule/ExampleModule.py -f <filename> -a <add_custom_message> -m <message_to_add> -o <output_filename>
+#commandLine when run with source in module zip/taskLib:
+#commandLine=<python_3.6> <libdir>ExampleModule.py -f <filename> -a <add_custom_message> -m <message_to_add> -o <output_filename>
+job.docker.image=genepattern/example-module:2
 cpuType=any
 description=This is an example GenePattern module written in Python 3. It can be used as a template for future modules. It reads a file and potentially adds a line of text
 fileFormat=txt
