- galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 2e50f6: It's annual cert update day
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2e50f6845a814a8b59ce9252b50ad3fcd19eb07e https://github.com/galaxyproject/usegalaxy-playbook/commit/2e50f6845a814a8b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M env/common/files/ssl/radegast.galaxyproject.org_cert.pem M env/common/files/ssl/usegalaxy.org_cert.pem M env/common/files/ssl/wildcard_cert.pem M env/common/group_vars/sslservers/vault.yml Log Message: ----------- It's annual cert update day **NOTE:** This service has 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] 222225: Fix selenium test selectors for alert messages
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 222225d3b017b4af457eb5c59248145899bc01ef https://github.com/galaxyproject/galaxy/commit/222225d3b017b4af457eb5c59248… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M test/galaxy_selenium/navigation.yml Log Message: ----------- Fix selenium test selectors for alert messages Commit: 47ad50e1d7738e443c96226f6abe5475c83ef32e https://github.com/galaxyproject/galaxy/commit/47ad50e1d7738e443c96226f6abe… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M templates/user/register.mako Log Message: ----------- Align legacy registration mako Commit: d29e3fc3bed92f856d140241fc0807f7283eea5f https://github.com/galaxyproject/galaxy/commit/d29e3fc3bed92f856d140241fc08… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M templates/user/info.mako Log Message: ----------- Align legacy user info template Commit: e5186a811032a2c4e8f52865588a0d9033365768 https://github.com/galaxyproject/galaxy/commit/e5186a811032a2c4e8f52865588a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M templates/webapps/galaxy/history/share.mako Log Message: ----------- Align legacy history sharing mako Commit: af05cb480b1c49b4cac560cfc086e9638ab7fb1b https://github.com/galaxyproject/galaxy/commit/af05cb480b1c49b4cac560cfc086… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M templates/user/info.mako M templates/user/register.mako M templates/webapps/galaxy/history/share.mako M test/galaxy_selenium/navigation.yml Log Message: ----------- Merge pull request #6881 from guerler/fix_selenium Fix selenium test selectors for alert messages Compare: https://github.com/galaxyproject/galaxy/compare/fbe9e97f19d6...af05cb480b1c **NOTE:** This service has 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] d19eff: One last batch of PRs.
by GitHub 17 Oct '18

17 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: d19effdf3c042538ffa0ba1351a2f3433ad19fd1 https://github.com/galaxyproject/galaxy/commit/d19effdf3c042538ffa0ba1351a2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- One last batch of PRs. Commit: 89fbe9c9344d1e8ad88fe88a0685cf85aa1edcb3 https://github.com/galaxyproject/galaxy/commit/89fbe9c9344d1e8ad88fe88a0685… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M doc/source/releases/18.09.rst Log Message: ----------- Merge pull request #6890 from dannon/18.09_release_notes_updates [18.09] One last batch of PRs added to RN Compare: https://github.com/galaxyproject/galaxy/compare/d4e2f6d59e15...89fbe9c9344d **NOTE:** This service has 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] 116ce0: Specify `GET` action for cloudauthz index.
by GitHub 16 Oct '18

16 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 116ce0ddf51654cfbb0923e7afc1ae5b035bd602 https://github.com/galaxyproject/galaxy/commit/116ce0ddf51654cfbb0923e7afc1… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Specify `GET` action for cloudauthz index. Commit: 612e6fc1cfb85e879f846cba90753a50182da5b4 https://github.com/galaxyproject/galaxy/commit/612e6fc1cfb85e879f846cba9075… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Specify `POST` action for cloudauthz create action. Commit: 83bfdf3c95a8ec7afe25b84867ade4f9dca4bd85 https://github.com/galaxyproject/galaxy/commit/83bfdf3c95a8ec7afe25b84867ad… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Unify `create` and `index` cloudauthz apis. Commit: aa20778e0f51b538af684c6b7fc2f39d998c0fb9 https://github.com/galaxyproject/galaxy/commit/aa20778e0f51b538af684c6b7fc2… Author: vahid <jalili.vahid(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/api/cloudauthz.py Log Message: ----------- remove `/create` from cloudauthz create api docstring. Commit: 73f691e5b51249b71b5f21b1f0faeea102b1c725 https://github.com/galaxyproject/galaxy/commit/73f691e5b51249b71b5f21b1f0fa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py Log Message: ----------- reword to reflect refactor Commit: fbe9e97f19d6f200cdac2548ae5c60e4b9687334 https://github.com/galaxyproject/galaxy/commit/fbe9e97f19d6f200cdac2548ae5c… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/managers/cloud.py M lib/galaxy/webapps/galaxy/api/cloudauthz.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Merge pull request #6876 from VJalili/refactor_cloud_authz_api Specify POST and GET actions for cloudauthz API actions Compare: https://github.com/galaxyproject/galaxy/compare/2310a509b2af...fbe9e97f19d6 **NOTE:** This service has 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] f8c48b: Username filtering for published workflows
by GitHub 16 Oct '18

16 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f8c48b83d2fadc8e4df008ce0f0e37f173a07b9d https://github.com/galaxyproject/galaxy/commit/f8c48b83d2fadc8e4df008ce0f0e… Author: almahmoud <amahmou4(a)jhu.edu> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Username filtering for published workflows Commit: 2310a509b2afdd1903a6a00c3df749b4884e66ab https://github.com/galaxyproject/galaxy/commit/2310a509b2afdd1903a6a00c3df7… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js Log Message: ----------- Merge pull request #6882 from almahmoud/published_workflow_bug Username filtering for published workflows Compare: https://github.com/galaxyproject/galaxy/compare/f4088c89a0b1...2310a509b2af **NOTE:** This service has 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] 429c29: History name not escaped
by GitHub 16 Oct '18

16 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 429c29a67166e0718776aee63ee709c60b6130bf https://github.com/galaxyproject/galaxy/commit/429c29a67166e0718776aee63ee7… Author: almahmoud <amahmou4(a)jhu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- History name not escaped Commit: f4088c89a0b110a648fe8f504ff4f26669c63613 https://github.com/galaxyproject/galaxy/commit/f4088c89a0b110a648fe8f504ff4… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #6871 from almahmoud/rename-bug History name not escaped Compare: https://github.com/galaxyproject/galaxy/compare/fb0f792f8d50...f4088c89a0b1 **NOTE:** This service has 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] a60f5f: Indicate language in client docs to enable syntax ...
by GitHub 16 Oct '18

16 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a60f5f6a89bc8139d2f72534f6819bcbcb9cfcc4 https://github.com/galaxyproject/galaxy/commit/a60f5f6a89bc8139d2f72534f681… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-10-10 (Wed, 10 Oct 2018) Changed paths: M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md Log Message: ----------- Indicate language in client docs to enable syntax highlighting. Enables syntax highlighting for code blocks in .md files. Commit: 39654146723109d11b33f24c93581feeb36327db https://github.com/galaxyproject/galaxy/commit/39654146723109d11b33f24c9358… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md Log Message: ----------- Minor updates to client dir: indicate language, add/update readme. 1. Add 'vue' as language to .md files in client/galaxy/docs. 2. Add README.md to docs directory. 3. Update main client README.md (LESS >> Sass). Commit: fb0f792f8d50e81b3a2c8b6b9ff49252377c5114 https://github.com/galaxyproject/galaxy/commit/fb0f792f8d50e81b3a2c8b6b9ff4… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/README.md A client/galaxy/docs/README.md M client/galaxy/docs/bootstrap.md M client/galaxy/docs/galaxy-buttons.md M client/galaxy/docs/galaxy-forms.md M client/galaxy/docs/galaxy-masthead.md M client/galaxy/docs/galaxy-menus.md M client/galaxy/docs/galaxy-messages.md M client/galaxy/docs/galaxy-panels.md M client/galaxy/docs/galaxy-tables.md M client/galaxy/docs/galaxy-tabs.md Log Message: ----------- Merge pull request #6848 from ic4f/dev Indicate language in client docs to enable syntax highlighting. Compare: https://github.com/galaxyproject/galaxy/compare/1e09f234e77c...fb0f792f8d50 **NOTE:** This service has 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] 67ee35: Use small button for editable text fields in histo...
by GitHub 16 Oct '18

16 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 67ee35874e65e5d2bc40caa7fd3cf143bce084c5 https://github.com/galaxyproject/galaxy/commit/67ee35874e65e5d2bc40caa7fd3c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/ui/editable-text.js Log Message: ----------- Use small button for editable text fields in history annotation Commit: 23541fcf2ccc87c22c5529020031f7a5cacfe100 https://github.com/galaxyproject/galaxy/commit/23541fcf2ccc87c22c5529020031… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/ui/editable-text.js Log Message: ----------- Float annotation button to the right Commit: 1e09f234e77cbca06c91dde4c1fc3af483ee6f1e https://github.com/galaxyproject/galaxy/commit/1e09f234e77cbca06c91dde4c1fc… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/galaxy/scripts/ui/editable-text.js Log Message: ----------- Merge pull request #6878 from guerler/fix_annotation_button Use small button for editable text fields in history annotation Compare: https://github.com/galaxyproject/galaxy/compare/168032ffc82d...1e09f234e77c **NOTE:** This service has 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] 4bd6d7: Add fix for rule editor element
by GitHub 16 Oct '18

16 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4bd6d71ed71643a9f28db9e41a6cf43e1af9a942 https://github.com/galaxyproject/galaxy/commit/4bd6d71ed71643a9f28db9e41a6c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Add fix for rule editor element Commit: da6c452a9d57ca81594c3c9966bfee19aa4bd01e https://github.com/galaxyproject/galaxy/commit/da6c452a9d57ca81594c3c9966bf… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Left align rule editor button Commit: 168032ffc82d0b19f07cbc101ad8d9273daa3d59 https://github.com/galaxyproject/galaxy/commit/168032ffc82d0b19f07cbc101ad8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-rules-edit.js Log Message: ----------- Merge pull request #6874 from guerler/fix_rules_editor Fix rule editor element alignment Compare: https://github.com/galaxyproject/galaxy/compare/d144523f7c29...168032ffc82d **NOTE:** This service has 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] 8edb74: Keep xlsx files compressed
by GitHub 15 Oct '18

15 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8edb7499c8d336d727fa751a2097d0356cf5bcbe https://github.com/galaxyproject/galaxy/commit/8edb7499c8d336d727fa751a2097… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Keep xlsx files compressed Fixes https://github.com/galaxyproject/galaxy/issues/6849 Commit: 0c7cc50e73827ac65eabf10400c90a644a15f10b https://github.com/galaxyproject/galaxy/commit/0c7cc50e73827ac65eabf10400c9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Only warn about multi-file zips if we don't keep the compressed archive Commit: 03073ed1249d2403994013d9f4486f85d7a23e80 https://github.com/galaxyproject/galaxy/commit/03073ed1249d2403994013d9f448… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Merge pull request #6867 from mvdbeek/fix_xlsx_unpacking [18.09] Keep xlsx files compressed Commit: b9a01761b03e4ad4c06e86a1250c2f33e62ae0be https://github.com/galaxyproject/galaxy/commit/b9a01761b03e4ad4c06e86a1250c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Do not traceback when uploading a TS repo with no changes Fix the following traceback when executing `planemo shed_update`: ``` galaxy.web.framework.decorators ERROR 2018-10-15 18:07:38,736 [p:30249,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 154, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/tool_shed/api/repositories.py", line 1116, in create_changeset_revision new_repo_alert File "lib/tool_shed/util/repository_content_util.py", line 64, in upload_tar undesirable_files_removed) File "lib/tool_shed/util/commit_util.py", line 225, in handle_directory_changes message=commit_message) File "lib/tool_shed/util/hg_util.py", line 65, in commit_changeset raise Exception(error_message) Exception: Error committing '/opt/galaxy/database/community_files/000/repo_1' to repository: Command '['hg', 'commit', '-u', u'earlhaminst', '-m', u'planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 22231ebc4e5e990c61243a3609b3347cf63fa024', '/opt/galaxy/database/community_files/000/repo_1']' returned non-zero exit status 1 Output was: nothing changed 127.0.0.1 - - [15/Oct/2018:18:07:38 +0100] "POST /api/repositories/adb5f5c93f827949/changeset_revision HTTP/1.1" 500 - "-" "python-requests/2.18.4" ``` Commit: d4e2f6d59e15bc06b35824201be30e95209596fb https://github.com/galaxyproject/galaxy/commit/d4e2f6d59e15bc06b35824201be3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #6875 from nsoranzo/release_18.09_fix_commit_changeset [18.09] Do not traceback when uploading a TS repo with no changes Commit: d144523f7c29ae03e48045fd1cff47b0efc50305 https://github.com/galaxyproject/galaxy/commit/d144523f7c29ae03e48045fd1cff… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-16 (Tue, 16 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge branch 'release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/519b994d40ef...d144523f7c29 **NOTE:** This service has 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] 89dafd: Fix styleguide; change permissions on jstree.scss.
by GitHub 15 Oct '18

15 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89dafdcfc00134f4453b987acf21b6790b0751d8 https://github.com/galaxyproject/galaxy/commit/89dafdcfc00134f4453b987acf21… Author: Sergey Golitsynskiy <sgolitsynskiy(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/style/scss/jstree.scss A static/style/blue/info_icon.svg Log Message: ----------- Fix styleguide; change permissions on jstree.scss. Styleguide: copy info_icon.svg from client/style/source_material/ to static/style/blue/. Permissions: change client/style/scss/jstree.scss to 644 (same as other scss files in directory.) Commit: 519b994d40ef758ba23d29bc6b84fbc5042aaba8 https://github.com/galaxyproject/galaxy/commit/519b994d40ef758ba23d29bc6b84… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/style/scss/jstree.scss A static/style/blue/info_icon.svg Log Message: ----------- Merge pull request #6879 from ic4f/styleguide_fix Fix styleguide; change permissions on jstree.scss. Compare: https://github.com/galaxyproject/galaxy/compare/1c466e037762...519b994d40ef **NOTE:** This service has 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] d5fd60: Updated slide rotation, Peaks to Genes tutorial is...
by GitHub 15 Oct '18

15 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d5fd607ad7f64cfd91690b07998ed87fdf110d98 https://github.com/galaxyproject/usegalaxy-playbook/commit/d5fd607ad7f64cfd… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: A env/common/files/galaxy/static/welcome_img/gtn-101.png M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- Updated slide rotation, Peaks to Genes tutorial is now Galaxy 101 **NOTE:** This service has 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] e9bb9c: Use card for display applications
by GitHub 15 Oct '18

15 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e9bb9cdfdddf39ebab8907aa06ed12cae0e55b83 https://github.com/galaxyproject/galaxy/commit/e9bb9cdfdddf39ebab8907aa06ed… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M templates/webapps/galaxy/admin/view_display_applications.mako Log Message: ----------- Use card for display applications Commit: 36604fc92397854b0f68e8c34e2edf2e349a199c https://github.com/galaxyproject/galaxy/commit/36604fc92397854b0f68e8c34e2e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M templates/admin/jobs.mako Log Message: ----------- Use card styles for manage jobs in admin panel Commit: 1ccb5a1f5c4bfc704b9b0464fb81705a1c03505e https://github.com/galaxyproject/galaxy/commit/1ccb5a1f5c4bfc704b9b0464fb81… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css M templates/admin/review_tool_migration_stages.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/view_display_applications.mako Log Message: ----------- Fix tool migration stages view Commit: 59eefbc2a456597840eb15e7dbc5bcc223d73529 https://github.com/galaxyproject/galaxy/commit/59eefbc2a456597840eb15e7dbc5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M templates/webapps/galaxy/admin/sanitize_whitelist.mako Log Message: ----------- Fix tool white listing view Commit: 1d680087471dee4cfe8573938f0d275db7addaaf https://github.com/galaxyproject/galaxy/commit/1d680087471dee4cfe8573938f0d… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/message.mako Log Message: ----------- Fix message style and repository monitoring Commit: 4e3ef50cb202ab43d7fb0ce3f9932f4da1666378 https://github.com/galaxyproject/galaxy/commit/4e3ef50cb202ab43d7fb0ce3f993… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M templates/message.mako Log Message: ----------- Fix custom message status Commit: cf4fca4b6a66488325dbc94edb67784b78ad9bb9 https://github.com/galaxyproject/galaxy/commit/cf4fca4b6a66488325dbc94edb67… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako Log Message: ----------- Add fixes for toolshed related makos Commit: 1c466e037762618ea33f9a5758469df9015c4047 https://github.com/galaxyproject/galaxy/commit/1c466e037762618ea33f9a575846… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/style/scss/ui.scss M static/style/blue/base.css M templates/admin/jobs.mako M templates/admin/review_tool_migration_stages.mako M templates/admin/tool_shed_repository/browse_repository.mako M templates/admin/tool_shed_repository/browse_tool_dependency.mako M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako M templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako M templates/admin/tool_shed_repository/manage_repository.mako M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako M templates/admin/tool_shed_repository/monitor_repository_installation.mako M templates/admin/tool_shed_repository/purge_repository_confirmation.mako M templates/admin/tool_shed_repository/reselect_tool_panel_section.mako M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako M templates/admin/tool_shed_repository/select_tool_panel_section.mako M templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako M templates/admin/tool_shed_repository/view_tool_metadata.mako M templates/admin/tool_shed_repository/view_workflow.mako M templates/message.mako M templates/webapps/galaxy/admin/manage_dependencies.mako M templates/webapps/galaxy/admin/sanitize_whitelist.mako M templates/webapps/galaxy/admin/view_display_applications.mako Log Message: ----------- Merge pull request #6868 from guerler/fix_display_applications Use card-styles for display applications, job manager and other admin views Compare: https://github.com/galaxyproject/galaxy/compare/c42cd4b71818...1c466e037762 **NOTE:** This service has 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] b9a017: Do not traceback when uploading a TS repo with no ...
by GitHub 15 Oct '18

15 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: b9a01761b03e4ad4c06e86a1250c2f33e62ae0be https://github.com/galaxyproject/galaxy/commit/b9a01761b03e4ad4c06e86a1250c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Do not traceback when uploading a TS repo with no changes Fix the following traceback when executing `planemo shed_update`: ``` galaxy.web.framework.decorators ERROR 2018-10-15 18:07:38,736 [p:30249,w:1,m:0] [uWSGIWorker1Core1] Uncaught exception in exposed API method: Traceback (most recent call last): File "lib/galaxy/web/framework/decorators.py", line 154, in decorator rval = func(self, trans, *args, **kwargs) File "lib/galaxy/webapps/tool_shed/api/repositories.py", line 1116, in create_changeset_revision new_repo_alert File "lib/tool_shed/util/repository_content_util.py", line 64, in upload_tar undesirable_files_removed) File "lib/tool_shed/util/commit_util.py", line 225, in handle_directory_changes message=commit_message) File "lib/tool_shed/util/hg_util.py", line 65, in commit_changeset raise Exception(error_message) Exception: Error committing '/opt/galaxy/database/community_files/000/repo_1' to repository: Command '['hg', 'commit', '-u', u'earlhaminst', '-m', u'planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 22231ebc4e5e990c61243a3609b3347cf63fa024', '/opt/galaxy/database/community_files/000/repo_1']' returned non-zero exit status 1 Output was: nothing changed 127.0.0.1 - - [15/Oct/2018:18:07:38 +0100] "POST /api/repositories/adb5f5c93f827949/changeset_revision HTTP/1.1" 500 - "-" "python-requests/2.18.4" ``` Commit: d4e2f6d59e15bc06b35824201be30e95209596fb https://github.com/galaxyproject/galaxy/commit/d4e2f6d59e15bc06b35824201be3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #6875 from nsoranzo/release_18.09_fix_commit_changeset [18.09] Do not traceback when uploading a TS repo with no changes Compare: https://github.com/galaxyproject/galaxy/compare/03073ed1249d...d4e2f6d59e15 **NOTE:** This service has 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] 6a94b1: Use fluid container for slider to get full width
by GitHub 15 Oct '18

15 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6a94b18a7b0866a3b12b4d3f0d80e4b4efb35a8b https://github.com/galaxyproject/galaxy/commit/6a94b18a7b0866a3b12b4d3f0d80… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Use fluid container for slider to get full width Commit: c42cd4b71818783c0d9a6aa77a96fb508e9e34a4 https://github.com/galaxyproject/galaxy/commit/c42cd4b71818783c0d9a6aa77a96… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-slider.js Log Message: ----------- Merge pull request #6870 from guerler/fix_slider_container Use fluid container for slider to get full width Compare: https://github.com/galaxyproject/galaxy/compare/2a422fa61f94...c42cd4b71818 **NOTE:** This service has 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] 8edb74: Keep xlsx files compressed
by GitHub 15 Oct '18

15 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 8edb7499c8d336d727fa751a2097d0356cf5bcbe https://github.com/galaxyproject/galaxy/commit/8edb7499c8d336d727fa751a2097… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Keep xlsx files compressed Fixes https://github.com/galaxyproject/galaxy/issues/6849 Commit: 0c7cc50e73827ac65eabf10400c90a644a15f10b https://github.com/galaxyproject/galaxy/commit/0c7cc50e73827ac65eabf10400c9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Only warn about multi-file zips if we don't keep the compressed archive Commit: 03073ed1249d2403994013d9f4486f85d7a23e80 https://github.com/galaxyproject/galaxy/commit/03073ed1249d2403994013d9f448… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-15 (Mon, 15 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/upload_util.py Log Message: ----------- Merge pull request #6867 from mvdbeek/fix_xlsx_unpacking [18.09] Keep xlsx files compressed Compare: https://github.com/galaxyproject/galaxy/compare/01f1f1b95fba...03073ed1249d **NOTE:** This service has 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] 20526c: Share ssh key generation across tests
by GitHub 14 Oct '18

14 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 20526ceb50b4406618de9cfbff771c86f6ea4af8 https://github.com/galaxyproject/galaxy/commit/20526ceb50b4406618de9cfbff77… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-14 (Sun, 14 Oct 2018) Changed paths: A test/base/ssh_util.py M test/integration/test_cli_runners.py M test/unit/test_remote_shell.py Log Message: ----------- Share ssh key generation across tests Closes https://github.com/galaxyproject/galaxy/issues/6860 Commit: 2a422fa61f946f7ca37d96dc18cbf765601e2924 https://github.com/galaxyproject/galaxy/commit/2a422fa61f946f7ca37d96dc18cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-14 (Sun, 14 Oct 2018) Changed paths: A test/base/ssh_util.py M test/integration/test_cli_runners.py M test/unit/test_remote_shell.py Log Message: ----------- Merge pull request #6865 from mvdbeek/share_key_function Share ssh key generation across tests Compare: https://github.com/galaxyproject/galaxy/compare/504cecfebb03...2a422fa61f94 **NOTE:** This service has 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/infrastructure-playbook] dd97c5: Stop reimplementing priority queueing for Slurm......
by GitHub 14 Oct '18

14 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: dd97c5e1a55da1013517e16d9a7b2d1e8f6f3695 https://github.com/galaxyproject/infrastructure-playbook/commit/dd97c5e1a55… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-14 (Sun, 14 Oct 2018) Changed paths: M env/tacc/group_vars/slurmservers.yml M env/tacc/templates/slurm/slurm.conf.j2 Log Message: ----------- Stop reimplementing priority queueing for Slurm... =/ **NOTE:** This service has 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] 1b1fef: Create container_resolvers_conf.xml.sample
by GitHub 13 Oct '18

13 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1b1fefca4598210b1045ceb6a6f2610a70517454 https://github.com/galaxyproject/galaxy/commit/1b1fefca4598210b1045ceb6a6f2… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-09-12 (Wed, 12 Sep 2018) Changed paths: A config/container_resolvers_conf.xml.sample Log Message: ----------- Create container_resolvers_conf.xml.sample Commit: 35b030486335ce802eb88510fd52d82a25ac0fb0 https://github.com/galaxyproject/galaxy/commit/35b030486335ce802eb88510fd52… Author: Pablo Moreno <pcm32(a)users.noreply.github.com> Date: 2018-09-13 (Thu, 13 Sep 2018) Changed paths: M config/container_resolvers_conf.xml.sample Log Message: ----------- Minor changes as requested Commit: b17665c9131878fb93225e613c863e1dc0411027 https://github.com/galaxyproject/galaxy/commit/b17665c9131878fb93225e613c86… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M config/container_resolvers_conf.xml.sample Log Message: ----------- Minor wording changes Commit: 02d5caae6915b1292b44870ca60361aff67816c4 https://github.com/galaxyproject/galaxy/commit/02d5caae6915b1292b44870ca603… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M config/container_resolvers_conf.xml.sample Log Message: ----------- Reword container to image where appropriate Commit: 504cecfebb0357e8a842a8b2bd11dfa7ffa6a4e1 https://github.com/galaxyproject/galaxy/commit/504cecfebb0357e8a842a8b2bd11… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-13 (Sat, 13 Oct 2018) Changed paths: A config/container_resolvers_conf.xml.sample Log Message: ----------- Merge pull request #6700 from pcm32/patch-1 Create container_resolvers_conf.xml.sample Compare: https://github.com/galaxyproject/galaxy/compare/ca95d7a26e70...504cecfebb03 **NOTE:** This service has 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] 4153f0: Add a special destination increasing the concurren...
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4153f00dec4071d657448f35ff780b6e2fbea18a https://github.com/galaxyproject/usegalaxy-playbook/commit/4153f00dec4071d6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Add a special destination increasing the concurrency limit for du novo align families **NOTE:** This service has 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] 1dd2f3: include one column of cards and one of twitter
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/new-welcome Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1dd2f3d65e621a15c111be0166f2ca559f2fa488 https://github.com/galaxyproject/usegalaxy-playbook/commit/1dd2f3d65e621a15… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- include one column of cards and one of twitter **NOTE:** This service has 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] 7246d5: Update Test
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7246d5f669b9cf58d6f71a5d4ebd11993daf05b3 https://github.com/galaxyproject/usegalaxy-playbook/commit/7246d5f669b9cf58… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test Commit: 3223a978e35a2140713d147c10d95d8f65d61021 https://github.com/galaxyproject/usegalaxy-playbook/commit/3223a978e35a2140… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main Commit: 0257084d6910b8d01759ea7f91a09c1a00093d1e https://github.com/galaxyproject/usegalaxy-playbook/commit/0257084d6910b8d0… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M env/main/group_vars/galaxyservers/vault.yml Log Message: ----------- Update admin users Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/1f66079a08f4...… **NOTE:** This service has 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] d791a2: Revert selective metadata flushing - seems to brea...
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: d791a2c80f3290d66c2252f29981a16a4459661b https://github.com/galaxyproject/galaxy/commit/d791a2c80f3290d66c2252f29981… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Revert selective metadata flushing - seems to break upload changes. Commit: f3da0864b45a3aa307c7fe9eeb8c5d26dd9c8527 https://github.com/galaxyproject/galaxy/commit/f3da0864b45a3aa307c7fe9eeb8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for regression #6856. Commit: 01f1f1b95fba671a2d92d7111676229a7ed5d58a https://github.com/galaxyproject/galaxy/commit/01f1f1b95fba671a2d92d7111676… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6858 from jmchilton/fix_metadata_revert [18.09] Revert selective metadata flushing - breaks multiple uploads/outputs. Commit: ca95d7a26e70ca02159febd971fa8b63c2667ab5 https://github.com/galaxyproject/galaxy/commit/ca95d7a26e70ca02159febd971fa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' into dev Compare: https://github.com/galaxyproject/galaxy/compare/ff32e5434145...ca95d7a26e70 **NOTE:** This service has 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] 1f6607: Test mutable configs
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1f66079a08f4dbd7b62aa74cfd10800312ef4912 https://github.com/galaxyproject/usegalaxy-playbook/commit/1f66079a08f4dbd7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-10-12 (Fri, 12 Oct 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 **NOTE:** This service has 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] d791a2: Revert selective metadata flushing - seems to brea...
by GitHub 12 Oct '18

12 Oct '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: d791a2c80f3290d66c2252f29981a16a4459661b https://github.com/galaxyproject/galaxy/commit/d791a2c80f3290d66c2252f29981… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-11 (Thu, 11 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py Log Message: ----------- Revert selective metadata flushing - seems to break upload changes. Commit: f3da0864b45a3aa307c7fe9eeb8c5d26dd9c8527 https://github.com/galaxyproject/galaxy/commit/f3da0864b45a3aa307c7fe9eeb8c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for regression #6856. Commit: 01f1f1b95fba671a2d92d7111676229a7ed5d58a https://github.com/galaxyproject/galaxy/commit/01f1f1b95fba671a2d92d7111676… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-12 (Fri, 12 Oct 2018) Changed paths: M lib/galaxy/model/metadata.py M test/api/test_tools.py A test/functional/tools/for_workflows/mapper_two.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6858 from jmchilton/fix_metadata_revert [18.09] Revert selective metadata flushing - breaks multiple uploads/outputs. Compare: https://github.com/galaxyproject/galaxy/compare/4805304e0bf3...01f1f1b95fba **NOTE:** This service has 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.

1 0