- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b861b9: implement basic cache on toolbox to_dict objects
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: b861b9ad4d693000ba8cf492ce6b1ff057db3d34 https://github.com/galaxyproject/galaxy/commit/b861b9ad4d693000ba8cf492ce6b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- implement basic cache on toolbox to_dict objects base the cache on absence of filters allow cache for users that don't opt in for filters Commit: 8a88cb9827b68e6795cf00496008e1aa189185ad https://github.com/galaxyproject/galaxy/commit/8a88cb9827b68e6795cf00496008… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- move the cache from toolbox level to tool level the cache remains toolbox-specific so it is stored within the toolbox object includes refactor thanks to eagle eyes Commit: a90c3a1d3f2c2a12f285f3c21e91ca364f81853e https://github.com/galaxyproject/galaxy/commit/a90c3a1d3f2c2a12f285f3c21e91… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #5583 from martenson/backport-toolbox-cache [18.01] Backport toolbox cache Compare: https://github.com/galaxyproject/galaxy/compare/50cd159d4c21...a90c3a1d3f2c

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[galaxyproject/galaxy] 93d5c5: Optimize count query in grids (part 1).
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 93d5c54946e992112841df3461512bbeb6f5c7e9 https://github.com/galaxyproject/galaxy/commit/93d5c54946e992112841df346151… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Optimize count query in grids (part 1). Many grid operations execute a complex query twice - once to produce the total number of rows and once to iterate through the selected parts of the data. This can be more optimal in many ways - this starts us down the path to addressing that by doing two things. The first thing it does is eliminates the query all together if paging is enabled but the user has opted to see "all" the rows. There was never a reason to execute the query in that case I don't think. The second thing it does is move the calculation of the count query until after the data has been generated - this isn't more optimal by itself but it allows us to potentially calculate the count as part of the main query. I've implemented this in a broken way @ https://github.com/galaxyproject/galaxy/commit/ea404721585b5f78da1b91e57e31… but I realized it was too broad an approach and doesn't work if certain kinds of joins are used in the initial query - but a more targetted approach on a per-grid basis could work I think and moving this code after allow us to potentially do that more easily in subsequent commits. Additionally I added a note - that I think it would be best to just return None as the number of pages and issue a second query to the same endpoint with the same arguments but with count_only=true added as a query request parameter so we can render the main grid faster and then render the paging elements after the second query finishes. This would feel more responsive I think. Commit: 50cd159d4c212a36b8d3861295125ef055a296d9 https://github.com/galaxyproject/galaxy/commit/50cd159d4c212a36b8d386129512… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M lib/galaxy/web/framework/helpers/grids.py Log Message: ----------- Merge pull request #5574 from jmchilton/optimize_count_query_1 [18.01] Optimize count query in grids (Part 1). Compare: https://github.com/galaxyproject/galaxy/compare/d8585f6a6f87...50cd159d4c21

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[galaxyproject/galaxy] c00e77: Fix lack of feedback when slow grids are loading d...
by GitHub 27 Feb '18

27 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: c00e772159f6a121bc4f7759fa57f48e79c48f32 https://github.com/galaxyproject/galaxy/commit/c00e772159f6a121bc4f7759fa57… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js Log Message: ----------- Fix lack of feedback when slow grids are loading data from the server. Fixes #5473 (after numerous other backend optimizations also). Commit: d8585f6a6f87735d072635495bd49047da746624 https://github.com/galaxyproject/galaxy/commit/d8585f6a6f87735d072635495bd4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-27 (Tue, 27 Feb 2018) Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js Log Message: ----------- Merge pull request #5582 from jmchilton/indicators [18.01] Fix lack of feedback when slow grids are loading data from the server. Compare: https://github.com/galaxyproject/galaxy/compare/c8407786f25c...d8585f6a6f87

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[galaxyproject/usegalaxy-playbook] dd4b14: Main mutable configs
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: dd4b1410d020827dde11de761d7c7ad575f4ba1e https://github.com/galaxyproject/usegalaxy-playbook/commit/dd4b1410d020827d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Main mutable configs

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[galaxyproject/usegalaxy-playbook] 9de278: Test mutable configs
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9de278cf3019b47e753bd6e5dfa660c8b67997d7 https://github.com/galaxyproject/usegalaxy-playbook/commit/9de278cf3019b47e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs

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[galaxyproject/usegalaxy-playbook] 0088bb: Mutable configs for new tool installs
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0088bb471eedd62aade63ebe54bfd958e67887c4 https://github.com/galaxyproject/usegalaxy-playbook/commit/0088bb471eedd62a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs for new tool installs

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[galaxyproject/usegalaxy-playbook] 95baed: Updated lastz.
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 95baede7590b49cc84b4ce2d105b924091e56bc2 https://github.com/galaxyproject/usegalaxy-playbook/commit/95baede7590b49cc… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated lastz.

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[galaxyproject/usegalaxy-playbook] a3feca: update MTS
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a3feca909a532438a65302bb71c927bc44188393 https://github.com/galaxyproject/usegalaxy-playbook/commit/a3feca909a532438… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/toolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update MTS

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[galaxyproject/usegalaxy-playbook] c72e72: update tts
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c72e7203b1cbb8419957e56c4bf0f67abbd772f0 https://github.com/galaxyproject/usegalaxy-playbook/commit/c72e7203b1cbb841… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update tts Commit: f2054837373e14d18ad4dcf0399ea085bc19c68d https://github.com/galaxyproject/usegalaxy-playbook/commit/f2054837373e14d1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/common/templates/nginx/toolshed.j2 Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/c3fd2231c3a6...…

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[galaxyproject/usegalaxy-playbook] c3fd22: Remove packed static route from TTS nginx
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c3fd2231c3a6d4bb14457ab057716a928f2aec55 https://github.com/galaxyproject/usegalaxy-playbook/commit/c3fd2231c3a6d4bb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/common/templates/nginx/toolshed.j2 Log Message: ----------- Remove packed static route from TTS nginx

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[galaxyproject/usegalaxy-playbook] b985a8: Updated Hisat2
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b985a826e22147b34abfa805611364a1760daa85 https://github.com/galaxyproject/usegalaxy-playbook/commit/b985a826e22147b3… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Updated Hisat2

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[galaxyproject/galaxy] d9d8f5: Eliminate precreated datasets concept in upload AP...
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d9d8f5d327827758d8d1cbe19b7cee84acc66071 https://github.com/galaxyproject/galaxy/commit/d9d8f5d327827758d8d1cbe19b7c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M tools/data_source/upload.xml Log Message: ----------- Eliminate precreated datasets concept in upload API. Was used by the async controller in the past I think (https://github.com/galaxyproject/galaxy/blob/v13.01/lib/galaxy/webapps/gala…) but doesn't seem to be used now. Commit: 73a0d72e0c98dfdcfdb60e228f757b4ea3967be1 https://github.com/galaxyproject/galaxy/commit/73a0d72e0c98dfdcfdb60e228f75… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/actions/library.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/parameters/grouping.py M tools/data_source/upload.xml Log Message: ----------- Merge pull request #5604 from jmchilton/persist_uploads_remove Eliminate precreated datasets concept in upload API. Compare: https://github.com/galaxyproject/galaxy/compare/2af4091e42b6...73a0d72e0c98

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[galaxyproject/galaxy] e3ced2: Fix migration 0137's downgrade -- previously faile...
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: e3ced2c669485f76eae7fcfb3b32aa048730964d https://github.com/galaxyproject/galaxy/commit/e3ced2c669485f76eae7fcfb3b32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py Log Message: ----------- Fix migration 0137's downgrade -- previously failed to select the correct column to drop Commit: c8407786f25c98c87f441f15222f72eeea4edc72 https://github.com/galaxyproject/galaxy/commit/c8407786f25c98c87f441f15222f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py Log Message: ----------- Merge pull request #5605 from dannon/migrate_fix [18.01] Fix migration 0137's downgrade Compare: https://github.com/galaxyproject/galaxy/compare/fc52fe5c6270...c8407786f25c

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[galaxyproject/galaxy] 291527: Update to latest galaxy-lib.
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 291527226755f7cf3210bb2f2d550ee1248184cd https://github.com/galaxyproject/galaxy/commit/291527226755f7cf3210bb2f2d55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-25 (Sun, 25 Feb 2018) Changed paths: M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/command.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Update to latest galaxy-lib. Includes: - Fixes for multi-requirement container building via mulled via https://github.com/galaxyproject/galaxy-lib/pull/84. - Fixes for Conda search problems https://github.com/galaxyproject/galaxy-lib/pull/83. - Updates to CWL library support https://github.com/galaxyproject/galaxy-lib/pull/78. - Make bz2file dependency optional (xref https://github.com/galaxyproject/galaxy-lib/pull/79) - Python 3 fixes for path stuff - runtime fixes caught because galaxy-lib runs tests using Python 3 https://github.com/galaxyproject/galaxy-lib/pull/85/commits/c056e39451ca8b4… and https://github.com/galaxyproject/galaxy-lib/pull/85/commits/c7cc9caba389770…) - Python 3 fix for linter (https://github.com/galaxyproject/galaxy-lib/pull/88/commits/17d167662cda2ae…) Commit: a6c8317d1d5d1eaa633c8a06d2ba9cd02c472716 https://github.com/galaxyproject/galaxy/commit/a6c8317d1d5d1eaa633c8a06d2ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-25 (Sun, 25 Feb 2018) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Bring in Nicola's Python 3 fixes. https://github.com/galaxyproject/galaxy-lib/commit/fcfb1aed1a08760857d5154a… https://github.com/galaxyproject/galaxy-lib/commit/704b2400a5cbfdb49d60508c… Commit: 2af4091e42b621720602734db5e408f28fe64fe4 https://github.com/galaxyproject/galaxy/commit/2af4091e42b621720602734db5e4… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/command.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #5602 from jmchilton/galaxy-lib-update-20180223 Update against galaxy-lib Compare: https://github.com/galaxyproject/galaxy/compare/91a0c0342166...2af4091e42b6

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[galaxyproject/galaxy] 8c80ce: move the cache from toolbox level to tool level
by GitHub 25 Feb '18

25 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8c80ce73b0c581426fa71baa4005ce6a11930fd1 https://github.com/galaxyproject/galaxy/commit/8c80ce73b0c581426fa71baa4005… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- move the cache from toolbox level to tool level the cache remains toolbox-specific so it is stored within the toolbox object includes refactor thanks to eagle eyes Commit: 91a0c0342166d0a615a265b326b219df88c99aa0 https://github.com/galaxyproject/galaxy/commit/91a0c0342166d0a615a265b326b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-25 (Sun, 25 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #5600 from martenson/move-cache-deeper move the cache from toolbox level to the tool level Compare: https://github.com/galaxyproject/galaxy/compare/f354b9d3f589...91a0c0342166

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[galaxyproject/usegalaxy-playbook] 026989: Disable additional GenomeSpace tools
by GitHub 23 Feb '18

23 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 026989f9e41990d5d2374134e07a5925fbd7b071 https://github.com/galaxyproject/usegalaxy-playbook/commit/026989f9e41990d5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/main/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/config/tool_conf.xml Log Message: ----------- Disable additional GenomeSpace tools

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[galaxyproject/usegalaxy-playbook] 81b6ba: Main mutable configs
by GitHub 23 Feb '18

23 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 81b6badbfdf7383ce76faa54029676f0202f992c https://github.com/galaxyproject/usegalaxy-playbook/commit/81b6badbfdf7383c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Main mutable configs Commit: dbf235bc8e64bbbf43f472dc255af3628ca685de https://github.com/galaxyproject/usegalaxy-playbook/commit/dbf235bc8e64bbbf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/main/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/config/tool_conf.xml Log Message: ----------- Temporarily disable GenomeSpace Importer due to problems Commit: b1294a3daa9b184807ee530b22e7b4aac0f3ebeb https://github.com/galaxyproject/usegalaxy-playbook/commit/b1294a3daa9b1848… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Temporarily disable GenomeSpace Importer due to problems with the tool Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/85499c50c73c...…

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[galaxyproject/usegalaxy-playbook] acb5d7: Run MAFFT as a multi job. Fixes #65
by GitHub 23 Feb '18

23 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: acb5d7af1c92c53a47f5dbef672819fddf2f4f5f https://github.com/galaxyproject/usegalaxy-playbook/commit/acb5d7af1c92c53a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run MAFFT as a multi job. Fixes #65 Commit: 85499c50c73cbee32cba99b89734d4d922d517d2 https://github.com/galaxyproject/usegalaxy-playbook/commit/85499c50c73cbee3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/574921ff0d98...…

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[galaxyproject/galaxy] 880603: Replace distutils.version with packaging.version
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8806030f53c2b9d0002505bf5193be88d7cff8f9 https://github.com/galaxyproject/galaxy/commit/8806030f53c2b9d0002505bf5193… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Replace distutils.version with packaging.version distutils under Python3 has this bug: https://bugs.python.org/issue14894 which causes this traceback: ``` Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 125, in __init__ self._configure_toolbox() File "lib/galaxy/config.py", line 930, in _configure_toolbox self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self) File "lib/galaxy/tools/__init__.py", line 232, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__ self._load_tool_panel() File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel self.__add_tool_to_tool_panel(section_val, section, section=True) File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel related_tool = self._lineage_in_panel(panel_dict, tool=tool) File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel lineage_tool_versions = reversed(tool_lineage.get_versions()) File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids return ["%s/%s" % (tool_id, version) for version in self.tool_versions] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions return sorted(self._tool_versions, key=LooseVersion) File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__ c = self._cmp(other) File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ``` when a tool version contains a letter in the "wrong" place (e.g. in the first position). Fix https://github.com/galaxyproject/galaxy/issues/5408 . Commit: fc52fe5c62700b4f8527e4edead0fba4e7cfe33f https://github.com/galaxyproject/galaxy/commit/fc52fe5c62700b4f8527e4edead0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #5588 from jmchilton/backport_packaging [18.01] Replace distutils.version with packaging.version Compare: https://github.com/galaxyproject/galaxy/compare/ce3b40cfc10e...fc52fe5c6270

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[galaxyproject/usegalaxy-playbook] 574921: Main: Increase Pulsar stream size
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 574921ff0d989aeb9e31e6229b59d0dadf72df29 https://github.com/galaxyproject/usegalaxy-playbook/commit/574921ff0d989aeb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/main/host_vars/br005.bridges.psc.edu.yml M env/main/host_vars/jetstream-iu0.galaxyproject.org.yml M env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/main/host_vars/login5.stampede.tacc.utexas.edu.yml Log Message: ----------- Main: Increase Pulsar stream size

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[galaxyproject/usegalaxy-playbook] 560c91: Main mutable config
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 560c9178467903dbe14f7643cceaf41c922f239d https://github.com/galaxyproject/usegalaxy-playbook/commit/560c9178467903db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Main mutable config Commit: abe7ecf5bc6c490883844dedcc43442aeefbe3fc https://github.com/galaxyproject/usegalaxy-playbook/commit/abe7ecf5bc6c4908… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M roles/usegalaxy_cvmfs/tasks/update.yml Log Message: ----------- Eliminate docker restart as it's no longer needed. Commit: 749403d897d4ed0cfa0ece17829208835edcb650 https://github.com/galaxyproject/usegalaxy-playbook/commit/749403d897d4ed0c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/main/group_vars/ftpservers/vars.yml M env/test/group_vars/ftpservers/vars.yml Log Message: ----------- Increase FTP upload limit to 75 GB Commit: dd1a8a790db92e7773c6853e7bbda3fff9611f7b https://github.com/galaxyproject/usegalaxy-playbook/commit/dd1a8a790db92e77… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/test/host_vars/br005.bridges.psc.edu.yml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/test/host_vars/login5.stampede.tacc.utexas.edu.yml Log Message: ----------- Increase Test Pulsar stream limits to 8 MB Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/8f88cb0342a4...…

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[galaxyproject/usegalaxy-playbook] 8f88cb: Main: Disable BioMart, enable @nuwang's GenomeSpac...
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8f88cb0342a4c5ceace6511ada0732657ee5b82d https://github.com/galaxyproject/usegalaxy-playbook/commit/8f88cb0342a4c5ce… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/main/files/galaxy/config/tool_conf.xml Log Message: ----------- Main: Disable BioMart, enable @nuwang's GenomeSpace updates, add new collection operations

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[galaxyproject/galaxy] 1656c7: Fix repeated fetching dataset permissions in dynam...
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 1656c7b429854323efda82accc4c190a965be8a3 https://github.com/galaxyproject/galaxy/commit/1656c7b429854323efda82accc4c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix repeated fetching dataset permissions in dynamic output collection. Commit: ce3b40cfc10e134d5acc477757404eba40ea6553 https://github.com/galaxyproject/galaxy/commit/ce3b40cfc10e134d5acc47775740… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #5578 from jmchilton/opt_dyn_collect [18.01] Fix repeated fetching dataset permissions in dynamic output collection. Compare: https://github.com/galaxyproject/galaxy/compare/d9372739376f...ce3b40cfc10e

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[galaxyproject/usegalaxy-playbook] 743d47: Installed circos, BLAST+, and PoreTools.
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 743d47222b6b27269dc76bf6702532906a273d3c https://github.com/galaxyproject/usegalaxy-playbook/commit/743d47222b6b2726… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Installed circos, BLAST+, and PoreTools.

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[galaxyproject/galaxy] 1a782e: Paginate published workflow grid.
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a782eb4eb29158a203df9e02b0195ecfe496e37 https://github.com/galaxyproject/galaxy/commit/1a782eb4eb29158a203df9e02b01… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Paginate published workflow grid. @martenson mentioned he prefers the look and feel of the published history grid so this replicates that and very likely will result in quicker rendering on usegalaxy.org - though we should verify this after it is deployed since the paginated grid do result in two big join queries instead of one big query - but I suspect rendering details on fewer objects (which includes fetching tag information from the db) will saved more than enough to make up for that. Commit: ff73cf2e6f8e1143e82681a9cfa97d769610f2c2 https://github.com/galaxyproject/galaxy/commit/ff73cf2e6f8e1143e82681a9cfa9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Handle header-only bam files correctly indicating there is no more data to fetch when chunking Commit: 34c5a1a1f39e4805b4b6e46d86e9db721c98199a https://github.com/galaxyproject/galaxy/commit/34c5a1a1f39e4805b4b6e46d86e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Two minor linting issues (deprecated e.message, unused var) Commit: 75b06187053de95f07fdbbb6caeaf3e52265238e https://github.com/galaxyproject/galaxy/commit/75b06187053de95f07fdbbb6caea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M tools/data_source/upload.py Log Message: ----------- Do not remove external path files during library uploads xref. https://github.com/galaxyproject/galaxy/pull/5264#issuecomment-367172820 Commit: f7f9c120eda7f9d735257eecaeb759ad50473f57 https://github.com/galaxyproject/galaxy/commit/f7f9c120eda7f9d735257eecaeb7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M test/integration/test_upload_configuration_options.py Log Message: ----------- Refactor BaseFtpUploadConfigurationTestCase._write_ftp_file() method Commit: f41230034689448abc6059d8e2771001961bafb9 https://github.com/galaxyproject/galaxy/commit/f41230034689448abc6059d8e277… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- No need to str() it; %s does this -- thanks @nsoranzo Commit: 117b4dcd6c503c51fb376c98ae8ba38d462d0301 https://github.com/galaxyproject/galaxy/commit/117b4dcd6c503c51fb376c98ae8b… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M test/base/populators.py M test/integration/test_upload_configuration_options.py Log Message: ----------- Update integration test to check external path files are not deleted after library upload This test would have failed before commit 75b06187053de95f07fdbbb6caeaf3e52265238e. Commit: 8afeffe95cc63832a6208e119cbfea4671a49a47 https://github.com/galaxyproject/galaxy/commit/8afeffe95cc63832a6208e119cbf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #5579 from dannon/fix_bam_nodata [18.01] Fix small bam (header-only) infinite fetching Commit: 8cc675eedd8bb895cf26cfc1fa5cbcc97e75f638 https://github.com/galaxyproject/galaxy/commit/8cc675eedd8bb895cf26cfc1fa5c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-21 (Wed, 21 Feb 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #5576 from jmchilton/workflow_paginate [18.01] Paginate published workflows grid. Commit: d9372739376f5d289740faae40e8790391d8d843 https://github.com/galaxyproject/galaxy/commit/d9372739376f5d289740faae40e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge pull request #5573 from nsoranzo/release_18.01_fix_filesystem_library_uploads [18.01] Do not remove external path files during library uploads Commit: f354b9d3f589e41020766968fe5827e99fd97c9d https://github.com/galaxyproject/galaxy/commit/f354b9d3f589e41020766968fe58… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6d94009cb359...f354b9d3f589

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