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Add InteractiveTools. #7494

Merged
merged 153 commits into from Aug 22, 2019
Merged

Add InteractiveTools. #7494

merged 153 commits into from Aug 22, 2019

Commits on Mar 8, 2019

  1. Add RealTimeTools. Currently working for docker in local runner.

    @blankenberg
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  2. Flake8

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  3. Update lib/galaxy/datatypes/realtime.py 

    Co-Authored-By: blankenberg <dan.blankenberg@gmail.com>
    @nsoranzo @blankenberg
    nsoranzo and blankenberg committed Mar 8, 2019
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Commits on Mar 9, 2019

  1. fix

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  2. fix

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Commits on Mar 13, 2019

  1. Make stop button in Active RealTimeTool list do something.

    @blankenberg
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Commits on Mar 14, 2019

  1. better handling of missing containers

    @blankenberg
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Commits on Mar 15, 2019

  1. merge dev into realtimetools

    @blankenberg
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  2. Update access to url_for().

    @blankenberg
    blankenberg committed Mar 15, 2019
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  3. import ordering

    @blankenberg
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Commits on Mar 16, 2019

  1. Only display view result message when view is available.

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Commits on Mar 20, 2019

  1. Add a ttl cache aware mapper to key_type_token_mapping.py.

    @blankenberg
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  2. Remove entries from realtimetool sqlite db when job has ended.

    @blankenberg
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  3. Simplify RealTimeTool model, associated entry points directly with job.

    @blankenberg
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  4. merge dev

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Commits on Mar 21, 2019

  1. remove debug statement

    @blankenberg
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  2. merge dev

    @blankenberg
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  3. comma

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  4. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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  5. fix for displaying realtimetool grid on refresh.

    @blankenberg
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  6. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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Commits on Mar 22, 2019

  1. Ports for yaml tools.

    @blankenberg
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  2. update tools xsd

    @blankenberg
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  3. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
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  4. over zealous delete key

    @blankenberg
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  5. flake

    @blankenberg
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  6. flake

    @blankenberg
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  7. naming update

    @blankenberg
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  8. move realtime rpc script to /scripts/realtime/

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  9. move realtime rpc script to /scripts/realtime/

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  10. Revert "move realtime rpc script to /scripts/realtime/" 

    This reverts commit 9ee4b9c.
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Commits on Mar 27, 2019

  1. rename rtt db migration

    @blankenberg
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  2. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
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Commits on Apr 2, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
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  2. rename realtimetool migration to higher version

    @blankenberg
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Commits on Apr 3, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
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  2. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
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Commits on Apr 8, 2019

  1. change version number of realtimetools migration

    @blankenberg
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  2. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
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  3. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
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  4. update migrate version of realtimetools

    @blankenberg
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  5. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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Commits on Apr 16, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
    blankenberg committed Apr 16, 2019
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  2. Remove inspection check, only do ports

    @blankenberg
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  3. Remove unneeded RealTimeTool datatype.

    @blankenberg
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  4. No more inspect, no more json needed.

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Commits on May 9, 2019

  1. Merge branch 'dev' of https://github.com/blankenberg/galaxy into real… 

    …timetools
    @blankenberg
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  2. Update rtt migrate version number

    @blankenberg
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  3. js-lint fix

    @blankenberg
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Commits on May 10, 2019

  1. remove extra _

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  2. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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Commits on May 13, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
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  2. Update RealTimeTool entry point definitions.

    @blankenberg
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  3. Update xsd

    @blankenberg
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  4. Enable templating of RealTime tools name, port, url.

    @blankenberg
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  5. Add docs and example job config.

    @blankenberg
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  6. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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  7. Remove unused import

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  8. change cellxgene Container to work with the IE tools

    @bgruening @blankenberg
    bgruening authored and blankenberg committed May 13, 2019
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  9. make entry_point_url parsing more robust

    @bgruening @blankenberg
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  10. add initial condor runner support

    @bgruening @blankenberg
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  11. add initial test tools for a interactive Vis

    @bgruening @blankenberg
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  12. add initial Jupyter notebook tool, this tool supports loading a noteb… 

    …ook and execute it automatically, with that it can run in a workflow
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  13. fix bug in setting the --net option during Docker startup

    @bgruening @blankenberg
    bgruening authored and blankenberg committed May 13, 2019
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  14. Update example RealTimeTools to use current syntax.

    @blankenberg
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  15. Merge pull request #5 from blankenberg/realtimetools-bg 

    Realtimetools bg
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  16. flake8 for lib/galaxy/jobs/runners/condor.py

    @blankenberg
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  17. mock

    @blankenberg
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  18. Update docs

    @blankenberg
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  19. Ports to test.

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  20. Doc formatting

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Commits on May 14, 2019

  1. More doc info

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  2. notes on resource consumption; and condor

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  3. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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Commits on May 15, 2019

  1. update docs

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  2. More doc formatting

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  3. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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  4. missing t

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Commits on May 20, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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  2. re.sub on cellxgene input name

    @blankenberg
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  3. Simplify set_name stuff in container.

    @jmchilton @blankenberg
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  4. Only set container if container exists, fixes tests failing due to Mo… 

    …ck object.
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  5. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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Commits on May 21, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into rt… 

    …t-tmp
    @blankenberg
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  2. Fix tool_util import 

    stupid .pyc files
    @blankenberg
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  3. Change default realtime prefix to something that isn't broken.

    @jmchilton
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  4. Refactor realtime entry point handling toward API usage. 

    - Add API entry point for fetching a target from an encoded entry point ID.
- Refactor target generation into a manager.
- Use galaxy.exceptions and exception handling instead of trans.show_error_message directly.
- Extend grid view to leverage this new API and use single-page error handling.
    @jmchilton
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  5. Move computing result_view for RTT to client.

    @jmchilton
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  6. Integration testing for RTT API hooks.

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Commits on May 22, 2019

  1. Rebase into intergration testsing..

    @jmchilton
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  2. Rework client polling & entry point index API for potential reuse in … 

    …the grid.

Fix links in the job monitor widget.
    @jmchilton
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  3. Make realtime tool grid actual links, poll on active.

    @jmchilton
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  4. Realtime Tools: Monitor for entrypoint ports in job script. 

    A few more pieces for local execution but more general, only requires a shared file system with Galaxy instead of direct access to docker host the job is running inside. Allows us to skip populating 'port' command in job destination. Eliminates a lot of condor hackiness - that implementation shares a lot more code with the local runner now.
    @jmchilton
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  5. Proper container killing when running jobs. 

    Rip out container_info container hacks for interactive tools, container killing should now just work with local job runner (or any job runners).
    @jmchilton
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Commits on May 28, 2019

  1. Add missing container_monitor package to previous commits.

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Commits on May 30, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
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  2. Lowercase import Vue from "vue";

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  3. flake8

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  4. jslint

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  5. flake

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Commits on May 31, 2019

  1. Update driver_util.py

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Commits on Jun 4, 2019

  1. Add container_montior_command to MockJobWrapper

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  2. montior --> monitor

    @blankenberg
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Commits on Jun 6, 2019

  1. juypter --> jupyter

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  2. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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Commits on Jun 17, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
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Commits on Jul 5, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
    blankenberg committed Jul 5, 2019
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  2. Change RealTimeTool to InteractiveTool in UI.

    @blankenberg
    blankenberg committed Jul 5, 2019
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  3. Change realtime tagset to entry_points.

    @blankenberg
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  4. Merge pull request #7 from blankenberg/interactivetools 

    Rename RealTimeTools to InteractiveTools
    @blankenberg
    blankenberg committed Jul 5, 2019
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Commits on Jul 6, 2019

  1. interactive

    @blankenberg
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Commits on Jul 7, 2019

  1. Fix for check_for_entry_points when file exists, but is not fully pop… 

    …ulated yet
    @blankenberg
    blankenberg committed Jul 7, 2019
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  2. Pass through tool defined environment_variables to Docker.

    @blankenberg
    blankenberg committed Jul 7, 2019
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  3. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
    blankenberg committed Jul 7, 2019
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  4. from galaxy.web.base.controller import is now from galaxy.webapps.bas… 

    …e.controller import
    @blankenberg
    blankenberg committed Jul 7, 2019
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  5. Add 404 when InteractiveTool route doesn't exist or can't be accessed

    @blankenberg
    blankenberg committed Jul 7, 2019
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  6. Flake

    @blankenberg
    blankenberg committed Jul 7, 2019
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  7. Add ability to strip whitespace from tool environment_variables.

    @blankenberg
    blankenberg committed Jul 7, 2019
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Commits on Jul 8, 2019

  1. Fix for fetching strip if not defined

    @blankenberg
    blankenberg committed Jul 8, 2019
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Commits on Jul 11, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
    blankenberg committed Jul 11, 2019
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Commits on Jul 25, 2019

  1. Don't set user in example interactive tool job_conf.xml

    @blankenberg
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  2. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
    blankenberg committed Jul 25, 2019
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Commits on Aug 11, 2019

  1. add a bunch of ITs

    @bgruening
    bgruening committed Aug 11, 2019
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  2. some small changes

    @bgruening
    bgruening committed Aug 11, 2019
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Commits on Aug 12, 2019

  1. Add API_KEY, GALAXY_URL, and fix HISTORY_ID envars 

    in interactive_tool_juypter_notebook.xml
    @blankenberg
    blankenberg committed Aug 12, 2019
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  2. Merge pull request galaxyproject#72 from blankenberg/patch-1 

    Add API_KEY, GALAXY_URL, and fix HISTORY_ID envars
    @bgruening
    bgruening committed Aug 12, 2019
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  3. Fix websockets in interactive_tool_bam_iobio.xml

    @blankenberg
    blankenberg committed Aug 12, 2019
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Commits on Aug 13, 2019

  1. Merge pull request galaxyproject#73 from blankenberg/patch-1 

    Fix websockets in interactive_tool_bam_iobio.xml
    @bgruening
    bgruening committed Aug 13, 2019
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  2. fixes for askomics IT

    @abretaud
    abretaud committed Aug 13, 2019
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  3. Merge pull request galaxyproject#75 from abretaud/it_askoko 

    Fixes for askomics IT
    @bgruening
    bgruening committed Aug 13, 2019
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  4. Update galaxy.yml.realtime example with outputs_to_working_directory:… 

    … true
    @blankenberg
    blankenberg committed Aug 13, 2019
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  5. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
    blankenberg committed Aug 13, 2019
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Commits on Aug 14, 2019

  1. remove complexity from ipython wrapper, not needed for this version

    @bgruening
    bgruening committed Aug 14, 2019
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  2. enhance documentation for developers

    @bgruening
    bgruening committed Aug 14, 2019
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  3. add some more comments

    @bgruening
    bgruening committed Aug 14, 2019
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  4. cleanup comments

    @blankenberg
    blankenberg committed Aug 14, 2019
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  5. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
    blankenberg committed Aug 14, 2019
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  6. update migration script version

    @blankenberg
    blankenberg committed Aug 14, 2019
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  7. Merge pull request #8 from bgruening/it 

    migrating a few more interactive environments to interactive tools
    @blankenberg
    blankenberg committed Aug 14, 2019
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Commits on Aug 20, 2019

  1. Merge branch 'dev' of https://github.com/galaxyproject/galaxy into re… 

    …altimetools
    @blankenberg
    blankenberg committed Aug 20, 2019
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  2. Make InteractiveTools enable-able.

    @blankenberg
    blankenberg committed Aug 20, 2019
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  3. minor typo

    @blankenberg
    blankenberg committed Aug 20, 2019
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  4. interactive_tool_juypter_notebook.xml -> interactive_tool_jupyter_not… 

    …ebook.xml
    @blankenberg
    blankenberg committed Aug 20, 2019
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  5. Add requires_domain to entry_point. Default is False. Currently only … 

    …True works.
    @blankenberg
    blankenberg committed Aug 20, 2019
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  6. Set requires_domain="True" for all examples.

    @blankenberg
    blankenberg committed Aug 20, 2019
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  7. Add warning on backwards compatibility of __app__ in future.

    @blankenberg
    blankenberg committed Aug 20, 2019
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  8. FIXME note on user's API key in tool.

    @blankenberg
    blankenberg committed Aug 20, 2019
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  9. Update galaxy tool XSD.

    @blankenberg
    blankenberg committed Aug 20, 2019
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  10. more realtime to interactivetools name changes

    @blankenberg
    blankenberg committed Aug 20, 2019
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  11. more realtimetool --> interactivetool

    @blankenberg
    blankenberg committed Aug 20, 2019
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  12. more realtimetool --> interactivetool

    @blankenberg
    blankenberg committed Aug 20, 2019
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  13. more realtimetool --> interactivetool

    @blankenberg
    blankenberg committed Aug 20, 2019
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Commits on Aug 21, 2019

  1. Fix get_hex for uuid4 in python3

    @blankenberg
    blankenberg committed Aug 21, 2019
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