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Install tools and workflow #3064

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merged 5 commits into from Aug 12, 2017

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commented Oct 18, 2016

import_tools is option and default is False.
If import_tools is True, install tools in workflow.

manabuishii added some commits Oct 18, 2016

Install tools and workflow
import_tools is option and default is False.
If import_tools is True, install tools in workflow.

@galaxybot galaxybot added the triage label Oct 18, 2016

@galaxybot galaxybot added this to the 16.10 milestone Oct 18, 2016

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commented Oct 19, 2016

Hi @manabuishii, thanks for this contribution, I think this is something a lot of people want.
I think #2823 is trying to achieve a very similar goal. Perhaps you could test this out and provide some feedback on whether it does what you would like to achieve here?

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commented Nov 7, 2016

Sorry long time no reply.

I need to check #2823 more detail and try with it.

Difference (a glimpse)
At least my PR is installed tool from toolshed when option is specified.
My PR is designed for Web API and using bioblend.

#2823 is not install tool from toolshed , it just return tool which is required install.
But I need to check more detail soon.

Future.
I want to import workflow and tool at once from web interface.
It'll be another PR.

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commented Nov 17, 2016

Currently I test #2823

/api/workflows?missing_tools=True

works fine.

It returns workflows with missing tools list.
After I install it disappear in return value.

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commented Nov 17, 2016

Still test #2823

/api/tool_shed_repositories/shed_repository

works file.

I can access different toolshed repository.
toolshed and testtoolshed

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commented Nov 17, 2016

I want to test GUI change of #2823
But I don't know how to check #2823 change in GUI ( Web interface )
Please tell me how to test GUI change.

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commented Nov 17, 2016

Main difference of my this PR and #2823 is that my PR is install missing tools.
#2823 is just display ( at least I my understand )

But my PR is just support /api/workflows not GUI (Web interface)

Option name is different from #2823

jmchilton added some commits Aug 10, 2017

Merge remote-tracking branch 'jmchilton/dev' into install_workflow_an…
…d_tools

Conflicts:
 lib/galaxy/webapps/galaxy/api/workflows.py
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commented Aug 10, 2017

@galaxybot test this

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commented Aug 10, 2017

I abused my access to merge with dev and pushed to this PR.

I also made a modification that requires the API user to be an admin to run this - since only admins are allowed to install shed repositories. I added a test case for this.

I'm 👍 on this - looks great - thanks for the contribution @manabuishii! I'll merge when the tests are done and I'm sorry for the delay.

@jmchilton jmchilton merged commit fc861cd into galaxyproject:dev Aug 12, 2017

4 of 5 checks passed

api test Build finished. 281 tests run, 0 skipped, 1 failed.
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continuous-integration/travis-ci/pr The Travis CI build passed
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framework test Build finished. 153 tests run, 0 skipped, 0 failed.
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integration test Build finished. 37 tests run, 0 skipped, 0 failed.
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toolshed test Build finished. 579 tests run, 0 skipped, 0 failed.
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