[WIP] GA4GH Task Execution Challenge Phase 2 Entry

project_templates/ga4gh_execution_challenge_phase_2/README.md

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+# GA4GH Tool Execution Challenge - Phase 2.
+
+This document describes how to use Planemo ([docs](http://planemo.readthedocs.io/en/latest/?badge=latest)
+| [github](https://github.com/galaxyproject/planemo)) to enter Phase 2 of the
+[GA4GH Tool Execution Challenge](https://www.synapse.org/#!Synapse:syn8507133/wiki/415976) using Galaxy.
+
+1. Register for [Synapse account](https://www.synapse.org/#!RegisterAccount:0).
+1. Become a [certified Synapse user](http://docs.synapse.org/articles/accounts_certified_users_and_profile_validation.html#certified-users) - requires passing a short quiz on data usage.
+1. [Register for the challenge](https://www.synapse.org/#!Synapse:syn8507133/wiki/415976).
+1. Setup a ``~/.synapseConfig`` file in your home directory.
+
+   ```
+   [authentication]
+   username: me@example.com
+   password: secret
+   ```
+
+1. Install Planemo and Synapse
+
+   ```
+   $ virtualenv planemo-venv; . planemo-venv/bin/activate
+   $ pip install -U pip
+   $ pip install planemo synapseclient
+   ```
+
+1. Pick a workflow, fetch it, run it, check it, and submit it (per-workflow instructions below).
+1. Go to the resulting workflow entry page and update it with your specific environment settings and ensure it and the relevant files are shared. 
+
+## The Workflows
+
+### hello_world
+
+https://www.synapse.org/#!Synapse:syn9630940
+
+A CWL script is distributed to fetch the workflow from Synapse. We will run this
+script using cwltool (installed with Planemo) - since it is a bit quicker than 
+starting up a Galaxy server. We will use Galaxy only to run the actual workflow.
+
+```
+mkdir hello_world
+cd hello_world
+cp ~/.synapseConfig .
+synapse get syn9733811
+synapse get syn9732885
+synapse get syn9770802
+cwltool --non-strict dockstore-tool-synapse-get.cwl hello_world_get.cwl.json
+```
+
+Use Planemo to run the ``hello_world.cwl`` workflow that results.
+
+```
+planemo --verbose run --docker --non_strict_cwl --no_dependency_resolution --output_directory `pwd` hello_world.cwl hello_world.cwl.json
+```
+
+Check the results using the checker workflow:
+
+```
+cwltool --non-strict hello_world_checker.cwl hello_world_checker.cwl.json
+```
+
+Update ``hello_world_submit.cwl.json`` with a ``team_name`` field and a ``parent_id`` and then
+submit using the submit worfklow. Create a new Project for the challenge (if you haven't 
+already) and a folder under that project to create a ``parent_id`` for this submission. If you
+wish to use the "GalaxyProject" team - contact John Chilton (jmchilton@gmail.com) to get added
+to the project.
+
+```
+cwltool --non-strict dockstore-tool-synapse-submit.cwl hello_world_submit.cwl.json
+```
+
+Wait for an e-mail with additional instructions and then go to the Synapse entry and update
+the fields in the wiki page generated for this new entry.
+
+### md5sum
+
+https://www.synapse.org/#!Synapse:syn10167920
+
+A CWL script is distributed to fetch the workflow from Synapse. We will run this
+script using cwltool (installed with Planemo) - since it is a bit quicker than 
+starting up a Galaxy server. We will use Galaxy only to run the actual workflow.
+
+
+```
+mkdir md5sum
+cd md5sum
+cp ~/.synapseConfig .
+synapse get syn9771740
+synapse get syn9732885
+synapse get syn9770802
+cwltool --non-strict dockstore-tool-synapse-get.cwl md5sum_get.cwl.json
+```
+
+Use Planemo to run the ``hello_world.cwl`` workflow that results.
+
+```
+planemo --verbose run --docker --non_strict_cwl --no_dependency_resolution --output_directory `pwd` md5sum.cwl md5sum.cwl.json
+```
+
+Check the results with the checker workflow:
+
+```
+cwltool md5sum_checker.cwl md5sum_checker.cwl.json
+cat results.json | grep -i overall
+```
+
+Update ``md5sum_submit.cwl.json`` with a ``team_name`` field and a ``parent_id`` and then
+submit using the submit worfklow. Create a new Project for the challenge (if you haven't 
+already) and a folder under that project to create a ``parent_id`` for this submission. If you
+wish to use the "GalaxyProject" team - contact John Chilton (jmchilton@gmail.com) to get added
+to the project.
+
+```
+cwltool --non-strict dockstore-tool-synapse-submit.cwl md5sum_submit.cwl.json
+```
+
+Wait for an e-mail with additional instructions and then go to the Synapse entry and update
+the fields in the wiki page generated for this new entry.
+
+### encode_mapping_workflow
+
+```
+mkdir encode_mapping
+cd encode_mapping
+cp ~/.synapseConfig .
+synapse get syn9732885
+synapse get -r syn10163025
+```
+
+### gdc_dnaseq_transform (WIP)
+
+This worklfow doesn't work yet - see open issues at https://github.com/common-workflow-language/galaxy.
+
+```
+mkdir gdc_dnaseq_transform
+cd gdc_dnaseq_transform
+cp ~/.synapseConfig .
+synapse get syn9962438
+synapse get syn9732885
+synapse get syn9770802 
+cwltool --non-strict dockstore-tool-synapse-get.cwl gdc_dnaseq_transform_get.cwl.json
+```
+
+This last step downloads around 12 GB of data so this may take some time.
+
+```
+planemo --verbose run --docker --cwl_galaxy_root ~/workspace/galaxy --output_directory `pwd` cwl/workflows/dnaseq/transform.cwl transform.cwl.json
+```
+
+### biowardrobe_chipseq_se (WIP)
+
+This worklfow doesn't work yet - see open issues at https://github.com/common-workflow-language/galaxy.
+
+mkdir biowardrobe_chipseq_se
+cd biowardrobe_chipseq_se
+cp ~/.synapseConfig .
+synapse get syn10204916
+synapse get syn9770802