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Docs for GA4GH Task Execution Challenge Phase 2.
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‎project_templates/ga4gh_execution_challenge_phase_2/README.md‎

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

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