October 2018 - galaxy-commits - lists.galaxyproject.org

[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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