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Updating for next release based on check list
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‎Dockerfile‎

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RUN mkdir /ExampleModule \
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&& chown gpuser /ExampleModule
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#switch to non-root before exiting so that we don't run as root on the server.
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#switch to non-root before exiting so that we don't run as root on the server, and copy all of the src files into the container.
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USER gpuser
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COPY src/*.py /ExampleModule/
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‎LICENSE‎

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----------------------------------------------------------------
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*** GENEPATTERN LICENSE AGREEMENT ***
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BSD 3-Clause License
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----------------------------------------------------------------
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The GenePattern ExampleModule is distributed under the following BSD-style license:
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Copyright (c) 2015-2021, Regents of the University of California & Broad Institute
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All rights reserved.
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Copyright (c) 2003-2021 Regents of the University of California and Broad Institute. All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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Redistribution and use in source and binary forms, with or without modification,
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are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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1. Redistributions of source code must retain the above copyright notice,
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this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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3. Neither the names of the Broad Institute, Inc., Massachusetts Institute of Technology
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nor the names of its contributors may be used to endorse or promote products derived
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from this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED AS IS. BROAD AND MIT MAKE NO EXPRESS OR IMPLIED
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REPRESENTATIONS OR WARRANTIES OF ANY KIND REGARDING THE SOFTWARE AND COPYRIGHT,
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INCLUDING, BUT NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
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PARTICULAR PURPOSE, CONFORMITY WITH ANY DOCUMENTATION, NONINFRINGEMENT, OR THE
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ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. IN NO EVENT SHALL
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BROAD, MIT, THE COPYRIGHT HOLDERS, OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
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INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
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BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA,
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OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF, HAVE REASON
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TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF SUCH DAMAGE.
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If, by operation of law or otherwise, any of the aforementioned warranty disclaimers
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are determined inapplicable, your sole remedy, regardless of the form of action,
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including, but not limited to, negligence and strict liability, shall be replacement
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of the software with an updated version if one exists.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎docs/v2/index.md‎

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**Contact**: [Forum Link](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!forum/genepattern-help)
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<!-- All modules have a version number associated with them (the last number on the LSID) that is used to differentiate between modules of the same name for reproducibility purposes. However, for publicly released software packages that are wrapped as GenePattern modules, sometimes this version number will be different that the version number of the algorithm itself (e.g. TopHat v7 in GenePattern uses version 2.0.8b of the TopHat algorithm). Since this information is often important to the user, the algorithm version field is an optional attribute that can be used to specify this different version number. Remove this field if not applicable -->
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**Algorithm Version**: OPTIONAL
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**Algorithm Version**: _OPTIONAL_ and Not applicable for this particular module
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<!-- Why use this module? What does it do? If this is one of a set of modules, how does this module fit in the set? How does it work? write overview as if you are explaining to a novice. Include any links or images which would serve to clarify -->
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## Summary
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<!-- links to your source repository **specific to the release version**, the Docker image used by the module (as specified in your manifest), and (if applicable) the sha link to the Dockerfile used to build your Docker image -->
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## Source Links
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* [The GenePattern ExampleModule v2 source repository](https://github.com/genepattern/ExampleModule/tree/v1)
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* ExampleModule v2 uses the [genepattern/docker-python36:0.4 Docker image](https://hub.docker.com/layers/25223888/genepattern/docker-python36/0.4/images/sha256-c251b34fc4e862535a246f9d74d71a385549b0545f9989d289f160e543b54ca5?context=explore)
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* [The Dockerfile used to build that image is here.](https://github.com/genepattern/docker-python36/blob/0.5/Dockerfile)
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* [The GenePattern ExampleModule v2 source repository](https://github.com/genepattern/ExampleModule/tree/v1.3)
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* ExampleModule v2 uses the [genepattern/example-module:2 Docker image](https://hub.docker.com/layers/150060459/genepattern/example-module/2/images/sha256-ae4fffff67672e46b251f954ad226b7ad99403c456c1c19911b6ac82f1a27f2f?context=explore)
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* [The Dockerfile used to build that image is here.](https://github.com/genepattern/ExampleModule/blob/v1.3/Dockerfile)
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## Parameters
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<!-- short description of the module parameters and their default values, as well as whether they are required -->
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<!-- provide links to example data so that users can see what input & output should look like and so that they and we can use it to test -->
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Input:
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[data_placeholder.txt](https://github.com/genepattern/ExampleModule/blob/v1/data/data_placeholder.txt)
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[data_placeholder.txt](https://github.com/genepattern/ExampleModule/blob/v1.3/data/data_placeholder.txt)
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Output:
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[created_file_ground_truth.txt](https://github.com/genepattern/ExampleModule/blob/v1/gpunit/output/basic_test/created_file_ground_truth.txt)
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[created_file_ground_truth.txt](https://github.com/genepattern/ExampleModule/blob/v1.3/gpunit/output/basic_test/created_file_ground_truth.txt)
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## Requirements
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<!--This section is typically used to list any special requirements for running the module, such as, language/operating system requirements and Docker images. -->
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Requires the [genepattern/docker-python36:0.4](https://hub.docker.com/layers/25223888/genepattern/docker-python36/0.4/images/sha256-c251b34fc4e862535a246f9d74d71a385549b0545f9989d289f160e543b54ca5?context=explore) Docker image.
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Requires the [genepattern/example-module:2 Docker image](https://hub.docker.com/layers/150060459/genepattern/example-module/2/images/sha256-ae4fffff67672e46b251f954ad226b7ad99403c456c1c19911b6ac82f1a27f2f?context=explore) Docker image.
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## License
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| Version | Release Date | Description |
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----------|--------------|---------------------------------------------|
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| 2 | May 17, 2021 | Added all required GP-Team Module release requirements and renamed as ExampleModule, from ABasicModule. |
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| 1.3 | May 17, 2021 | Added all required GP-Team Module release requirements and renamed as ExampleModule, from ABasicModule. |
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| 1 | May 1, 2018 | Initial version for team use. |

‎gpunit/basic_test.yml‎ renamed to ‎gpunit/ExampleModule_basic_diff_test.yml‎

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‎manifest‎

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#commandLine when run with source in module zip/taskLib:
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#commandLine=<python_3.6> <libdir>ExampleModule.py -f <filename> -a <add_custom_message> -m <message_to_add> -o <output_filename>
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job.docker.image=genepattern/example-module:2
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src.repo=https://github.com/genepattern/ExampleModule/tree/v1.3
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cpuType=any
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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
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fileFormat=txt
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taskDoc=doc.html
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[email protected]
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version=Renaming as ExampleModule
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version=Renaming as ExampleModule and updating to latest release standards

‎src/ExampleModule.py‎

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#!/usr/bin/env python3
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#NB - all of these import statements should specify their versions and be executed in a separate script at Docker build time.
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from ExampleModule_functions import *
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import argparse
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import humanfriendly

‎src/ExampleModule_command_line_call.py‎

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#!/usr/bin/env python3
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#NB - all of these import statements should specify their versions and be executed in a separate script at Docker build time.
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import os
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import sys
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from subprocess import call

‎src/ExampleModule_functions.py‎

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#!/usr/bin/env python3
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#NB - all of these import statements should specify their versions and be executed in a separate script at Docker build time.
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# Here is where I'd put my functions, if I had any!
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def empty_function():
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return

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