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[galaxyproject/galaxy] fb291e: check memory later
by GitHub 10 May '18

10 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: fb291eb530858c79c83be10502d4b78b585d77cb https://github.com/galaxyproject/galaxy/commit/fb291eb530858c79c83be10502d4… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- check memory later Commit: 765a834497ebfc555ac0de98cbbae9ad395f1c49 https://github.com/galaxyproject/galaxy/commit/765a834497ebfc555ac0de98cbba… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-07 (Mon, 07 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Memory statement and cd both before instrument_pre_commands Commit: 1343b04380b048dd75264c2ed9fb2ae7ca820d00 https://github.com/galaxyproject/galaxy/commit/1343b04380b048dd75264c2ed9fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix workflow step cloning Problem one is that passing the tool_state as the input payload doesn't preserve the tool state, adressed with the client-part fix. Then passing the tool state still has no effect since the state is properly recovered in `module_factory.from_dict`, but then overwritten by recovering the state starting with an empty dict. It looks like this isn't necessary as we call populate_state anyway when calling `module.get_config_form()`. Fixes https://github.com/galaxyproject/galaxy/issues/5879. Commit: 098f638d26355abe54c83bd43b8daf1078e1ccd3 https://github.com/galaxyproject/galaxy/commit/098f638d26355abe54c83bd43b8d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh Log Message: ----------- Merge pull request #5925 from erasche/cd-before-metrics [18.01] jobscript - check memory later Commit: 4f20aee2189218cfead67d0153cd579d5674d3eb https://github.com/galaxyproject/galaxy/commit/4f20aee2189218cfead67d0153cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Rebuild client for workflow step copy fix Commit: 5fa450dc9b9826ffc0bd0a3552a586a2dfcbb859 https://github.com/galaxyproject/galaxy/commit/5fa450dc9b9826ffc0bd0a3552a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore `populate_state`, but only execute if `tool_state` not given Commit: 250973eb46fc69baa6e8018c5f6e6e9552edd877 https://github.com/galaxyproject/galaxy/commit/250973eb46fc69baa6e8018c5f6e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #6085 from mvdbeek/fix_workflow_step_cloning [18.01] Fix workflow step cloning Commit: ef7d90a3dec1c0e517a196999d892b34af6896d1 https://github.com/galaxyproject/galaxy/commit/ef7d90a3dec1c0e517a196999d89… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-05-10 (Thu, 10 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Compare: https://github.com/galaxyproject/galaxy/compare/63abfd657a38...ef7d90a3dec1 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 07a34f: Add file missing file required for converting bz2 ...
by GitHub 09 May '18

09 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 07a34f8c5759fa9d609cd008524aaef473259762 https://github.com/galaxyproject/galaxy/commit/07a34f8c5759fa9d609cd008524a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml Log Message: ----------- Add file missing file required for converting bz2 compressed files. Should have been included with #5794. Commit: 63abfd657a38355357b476c044afa05d7d07b594 https://github.com/galaxyproject/galaxy/commit/63abfd657a38355357b476c044af… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml M lib/galaxy/datatypes/converters/gz_to_uncompressed.xml Log Message: ----------- Merge pull request #6101 from jmchilton/more_conversion_fixes [18.05] Add file missing file required for converting bz2 compressed files. Compare: https://github.com/galaxyproject/galaxy/compare/9ef3449f174a...63abfd657a38 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 1ac321: raise sloreq threshold from 1 to 3
by GitHub 09 May '18

09 May '18

Branch: refs/heads/sloreq Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1ac321f78dc7339ccce5d3965b65249fe15c609d https://github.com/galaxyproject/usegalaxy-playbook/commit/1ac321f78dc7339c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- raise sloreq threshold from 1 to 3 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 208d1d: Set the level for SLOREQs to 'warning'
by GitHub 09 May '18

09 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 208d1de2e13b84f6a9551cd7ca08b859a16be57e https://github.com/galaxyproject/galaxy/commit/208d1de2e13b84f6a9551cd7ca08… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Set the level for SLOREQs to 'warning' Commit: 9ef3449f174ab6128af3bab8bcde75b4cecdcca8 https://github.com/galaxyproject/galaxy/commit/9ef3449f174ab6128af3bab8bcde… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #6102 from dannon/sentry_add_type_tag [18.05] Set the level for SLOREQs to 'warning' Compare: https://github.com/galaxyproject/galaxy/compare/1f608a67de54...9ef3449f174a **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 770f83: update Main
by GitHub 09 May '18

09 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 770f83edec684dc3eefe56939cc0c38639f667fc https://github.com/galaxyproject/usegalaxy-playbook/commit/770f83edec684dc3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- update Main **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] a7e7ac: Escape tool names in the onclick event handlers fo...
by GitHub 09 May '18

09 May '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: a7e7ac723ff7379cf201be9b99acae95ebb8851d https://github.com/galaxyproject/galaxy/commit/a7e7ac723ff7379cf201be9b99ac… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Escape tool names in the onclick event handlers for the workflow editor's toolbox. Commit: 1f608a67de540e657d418ed2abf050c605f5fba1 https://github.com/galaxyproject/galaxy/commit/1f608a67de540e657d418ed2abf0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M templates/webapps/galaxy/workflow/editor.mako Log Message: ----------- Merge pull request #6099 from dannon/workflow_editor_escape [18.05] Escape tool names in the onclick event handlers for the workflow edit… Compare: https://github.com/galaxyproject/galaxy/compare/fba70530abf4...1f608a67de54 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 1343b0: Fix workflow step cloning
by GitHub 09 May '18

09 May '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 1343b04380b048dd75264c2ed9fb2ae7ca820d00 https://github.com/galaxyproject/galaxy/commit/1343b04380b048dd75264c2ed9fb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-08 (Tue, 08 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Fix workflow step cloning Problem one is that passing the tool_state as the input payload doesn't preserve the tool state, adressed with the client-part fix. Then passing the tool state still has no effect since the state is properly recovered in `module_factory.from_dict`, but then overwritten by recovering the state starting with an empty dict. It looks like this isn't necessary as we call populate_state anyway when calling `module.get_config_form()`. Fixes https://github.com/galaxyproject/galaxy/issues/5879. Commit: 4f20aee2189218cfead67d0153cd579d5674d3eb https://github.com/galaxyproject/galaxy/commit/4f20aee2189218cfead67d0153cd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Rebuild client for workflow step copy fix Commit: 5fa450dc9b9826ffc0bd0a3552a586a2dfcbb859 https://github.com/galaxyproject/galaxy/commit/5fa450dc9b9826ffc0bd0a3552a5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py Log Message: ----------- Restore `populate_state`, but only execute if `tool_state` not given Commit: 250973eb46fc69baa6e8018c5f6e6e9552edd877 https://github.com/galaxyproject/galaxy/commit/250973eb46fc69baa6e8018c5f6e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/workflow/workflow-node.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #6085 from mvdbeek/fix_workflow_step_cloning [18.01] Fix workflow step cloning Compare: https://github.com/galaxyproject/galaxy/compare/098f638d2635...250973eb46fc **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] d89c5a: Load tools from /cvmfs/sandbox.galaxyproject.org/
by GitHub 09 May '18

09 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d89c5a1d0597dfe4bad487d39da099c87eb306a7 https://github.com/galaxyproject/usegalaxy-playbook/commit/d89c5a1d0597dfe4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Load tools from /cvmfs/sandbox.galaxyproject.org/ **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 6373d3: fixed typo
by GitHub 09 May '18

09 May '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6373d352a83cb1a1f530cdad288ee90fb2b3ec48 https://github.com/galaxyproject/galaxy/commit/6373d352a83cb1a1f530cdad288e… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- fixed typo Commit: a53551448b756cc90305fad25101a0969b59c292 https://github.com/galaxyproject/galaxy/commit/a53551448b756cc90305fad25101… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge pull request #6094 from bernt-matthias/topic/collection-typo fixed small typo Compare: https://github.com/galaxyproject/galaxy/compare/c67c4b4b82dd...a53551448b75 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 79f7ea: Enable client building on MTS and work around node...
by GitHub 09 May '18

09 May '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 79f7ea0d7529f4abde999db569a344c14fa0136c https://github.com/galaxyproject/usegalaxy-playbook/commit/79f7ea0d7529f4ab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M env/common/_inc_client_build.yml A env/toolshed/_inc_client_build.yml Log Message: ----------- Enable client building on MTS and work around nodejs/node#20285 nodejs/node#20325 Commit: 08ba973f63f59b58c96749d955cc2f38810fa3c3 https://github.com/galaxyproject/usegalaxy-playbook/commit/08ba973f63f59b58… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-05-09 (Wed, 09 May 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- Update MTS to 18.05 Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/e14ec11f0429...… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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