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

[galaxyproject/usegalaxy-playbook] 37602f: Have Test load UCSC dbkeys from CVMFS
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 37602f74bf7b35e4dc4819db4bff287cd77ed916 https://github.com/galaxyproject/usegalaxy-playbook/commit/37602f74bf7b35e4… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M env/test/files/galaxy/config/tool_data_table_conf.xml Log Message: ----------- Have Test load UCSC dbkeys from CVMFS **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] c42ea4: Fixed monitor Proxy set function
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c42ea4d9c5e38bc365b54d97f51c96def0f3def7 https://github.com/galaxyproject/galaxy/commit/c42ea4d9c5e38bc365b54d97f51c… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/utils/installMonitor.js M client/webpack.config.js M client/yarn.lock Log Message: ----------- Fixed monitor Proxy set function Commit: 9b7b6ab04d4f0eaa6500cabacf632ef45acf5bcf https://github.com/galaxyproject/galaxy/commit/9b7b6ab04d4f0eaa6500cabacf63… Author: Mason <nerdinacan(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: A client/galaxy/scripts/libs/jquery.custom.js Log Message: ----------- Added jquery.custom.js to lib folder Commit: eb57469eef96f7225192128bd846237443e9b437 https://github.com/galaxyproject/galaxy/commit/eb57469eef96f7225192128bd846… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: A client/galaxy/scripts/libs/jquery.custom.js M client/galaxy/scripts/onload/index.js M client/galaxy/scripts/qunit/test.js M client/galaxy/scripts/qunit/tests/page_tests.js M client/galaxy/scripts/utils/installMonitor.js M client/webpack.config.js M client/yarn.lock Log Message: ----------- Merge pull request #6970 from Nerdinacan/jquery_bundle Normalized jquery bundle Compare: https://github.com/galaxyproject/galaxy/compare/a4f21fca773c...eb57469eef96 **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] 443170: optimize images with optipng
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 443170e9128cd785dcfc24f73bddc5bcc1035fa3 https://github.com/galaxyproject/galaxy/commit/443170e9128cd785dcfc24f73bdd… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/images/Armitagep_manhattan.png M client/galaxy/images/Armitagep_qqplot.png M client/galaxy/images/add_icon.png M client/galaxy/images/add_icon_dark.png M client/galaxy/images/aggregate_history1.png M client/galaxy/images/aggregate_history2.png M client/galaxy/images/bar_chart.png M client/galaxy/images/bed_warn.png M client/galaxy/images/closebox.png M client/galaxy/images/dat_points_table_brows_1.png M client/galaxy/images/data_empty.png M client/galaxy/images/data_error.png M client/galaxy/images/data_ok.png M client/galaxy/images/data_queued.png M client/galaxy/images/ddarrowsplit.png M client/galaxy/images/delete_tag_icon_gray.png M client/galaxy/images/delete_tag_icon_white.png M client/galaxy/images/documents-stack-faded.png M client/galaxy/images/dropdownarrow.png M client/galaxy/images/error_large.png M client/galaxy/images/error_small.png M client/galaxy/images/fetchTax.png M client/galaxy/images/form_body_bg.png M client/galaxy/images/fugue.png M client/galaxy/images/hatch-023858.png M client/galaxy/images/histogram.png M client/galaxy/images/histogram2.png M client/galaxy/images/history-buttons.png M client/galaxy/images/history-states.png M client/galaxy/images/info_large.png M client/galaxy/images/info_small.png M client/galaxy/images/kendall.png M client/galaxy/images/mag_glass.png M client/galaxy/images/masthead_bg.png M client/galaxy/images/mutation_visualization_example.png M client/galaxy/images/ok_large.png M client/galaxy/images/ok_small.png M client/galaxy/images/overview_arrows.png M client/galaxy/images/question-octagon-frame.png M client/galaxy/images/scatter.png M client/galaxy/images/scatterplot.png M client/galaxy/images/solid_qual.png M client/galaxy/images/sprite-fugue.png M client/galaxy/images/sprite-history-buttons.png M client/galaxy/images/sprite-history-states.png M client/galaxy/images/thumbtack_icon.png M client/galaxy/images/thumbtack_icon_dark.png M client/galaxy/images/wait_large.png M client/galaxy/images/wait_small.png Log Message: ----------- optimize images with optipng Commit: a4f21fca773c91032e11804e4a4c71646c213da0 https://github.com/galaxyproject/galaxy/commit/a4f21fca773c91032e11804e4a4c… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/images/Armitagep_manhattan.png M client/galaxy/images/Armitagep_qqplot.png M client/galaxy/images/add_icon.png M client/galaxy/images/add_icon_dark.png M client/galaxy/images/aggregate_history1.png M client/galaxy/images/aggregate_history2.png M client/galaxy/images/bar_chart.png M client/galaxy/images/bed_warn.png M client/galaxy/images/closebox.png M client/galaxy/images/dat_points_table_brows_1.png M client/galaxy/images/data_empty.png M client/galaxy/images/data_error.png M client/galaxy/images/data_ok.png M client/galaxy/images/data_queued.png M client/galaxy/images/ddarrowsplit.png M client/galaxy/images/delete_tag_icon_gray.png M client/galaxy/images/delete_tag_icon_white.png M client/galaxy/images/documents-stack-faded.png M client/galaxy/images/dropdownarrow.png M client/galaxy/images/error_large.png M client/galaxy/images/error_small.png M client/galaxy/images/fetchTax.png M client/galaxy/images/form_body_bg.png M client/galaxy/images/fugue.png M client/galaxy/images/hatch-023858.png M client/galaxy/images/histogram.png M client/galaxy/images/histogram2.png M client/galaxy/images/history-buttons.png M client/galaxy/images/history-states.png M client/galaxy/images/info_large.png M client/galaxy/images/info_small.png M client/galaxy/images/kendall.png M client/galaxy/images/mag_glass.png M client/galaxy/images/masthead_bg.png M client/galaxy/images/mutation_visualization_example.png M client/galaxy/images/ok_large.png M client/galaxy/images/ok_small.png M client/galaxy/images/overview_arrows.png M client/galaxy/images/question-octagon-frame.png M client/galaxy/images/scatter.png M client/galaxy/images/scatterplot.png M client/galaxy/images/solid_qual.png M client/galaxy/images/sprite-fugue.png M client/galaxy/images/sprite-history-buttons.png M client/galaxy/images/sprite-history-states.png M client/galaxy/images/thumbtack_icon.png M client/galaxy/images/thumbtack_icon_dark.png M client/galaxy/images/wait_large.png M client/galaxy/images/wait_small.png Log Message: ----------- Merge pull request #6980 from bgruening/optipng optimize images with optipng Compare: https://github.com/galaxyproject/galaxy/compare/b7c8bd47c907...a4f21fca773c **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] a2fcc8: Update Main
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a2fcc8d915037f895985c1553eee651b51eb0198 https://github.com/galaxyproject/usegalaxy-playbook/commit/a2fcc8d915037f89… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M env/main/files/galaxy/galaxy_version.yml Log Message: ----------- Update Main **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] dc9128: Fix traceback when starting under Python3 with ``g...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: dc9128213fbf4fd1d479fc94ace5b2416a5face5 https://github.com/galaxyproject/galaxy/commit/dc9128213fbf4fd1d479fc94ace5… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Fix traceback when starting under Python3 with ``galaxy.ini`` Update `paste` requirement to 3.0.4 to include: https://github.com/cdent/paste/pull/14 to fix the following traceback: ``` Starting server in PID 6792. Traceback (most recent call last): File "./scripts/paster.py", line 27, in <module> serve.run() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1055, in run invoke(command, command_name, options, args[1:]) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 1061, in invoke exit_code = runner.run(args) File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 226, in run result = self.command() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 676, in command serve() File "/opt/galaxy/lib/galaxy/util/pastescript/serve.py", line 653, in serve server(app) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 232, in server_wrapper **context.local_conf) File "/opt/galaxy/lib/galaxy/util/pastescript/loadwsgi.py", line 90, in fix_call val = callable(*args, **kw) File "/opt/galaxy/.venv3/lib/python3.5/site-packages/paste/httpserver.py", line 1358, in server_runner for name, value in kwargs.items(): RuntimeError: dictionary changed size during iteration galaxy.app DEBUG 2018-11-05 13:38:00,059 Shutting down ``` Commit: 6487d52d513b6351bd3e3e44e74e79c8f949919a https://github.com/galaxyproject/galaxy/commit/6487d52d513b6351bd3e3e44e74e… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt Log Message: ----------- Merge pull request #6978 from nsoranzo/release_18.09_paste [18.09] Fix traceback when starting under Python3 with ``galaxy.ini`` Compare: https://github.com/galaxyproject/galaxy/compare/9029b95e6979...6487d52d513b **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] 558335: Disable legacy late eager object store assignment ...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 5583358d1318a5cf9418cdb2a05962e3e3bb7e49 https://github.com/galaxyproject/usegalaxy-playbook/commit/5583358d1318a5cf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml Log Message: ----------- Disable legacy late eager object store assignment on Main since bugs should be fixed **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] ccb1e0: In enqueue, always set an object_store_id if one i...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: ccb1e08000759184b2ebc4d26b8e88ebe9b4c9c4 https://github.com/galaxyproject/galaxy/commit/ccb1e08000759184b2ebc4d26b8e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- In enqueue, always set an object_store_id if one isn't set. Tool actions other than the regular tool action (such as the upload ones) might not set an object store id even in the legacy mode. Commit: 9029b95e69795992ecf67f3ffdfa6384b52e1f3a https://github.com/galaxyproject/galaxy/commit/9029b95e69795992ecf67f3ffdfa… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #6969 from jmchilton/ensure_better [18.09] In enqueue, always set an object_store_id if one isn't set. Compare: https://github.com/galaxyproject/galaxy/compare/dbf5ef33604a...9029b95e6979 **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] 9c8108: Catch IOErrors when the k8s runner tries to collec...
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 9c81089ed1c9d5c434ecb991be8fd542bbe3c75e https://github.com/galaxyproject/galaxy/commit/9c81089ed1c9d5c434ecb991be8f… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Catch IOErrors when the k8s runner tries to collect job logs This commit should fix cases where successful job can't be marked as done by Galaxy because the logs have gone missing. Commit: ac7c2d0473d09e8a3b4b39734527a383835478ab https://github.com/galaxyproject/galaxy/commit/ac7c2d0473d09e8a3b4b39734527… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-17 (Wed, 17 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Print full job object to the DEBUG log if k8s runner finds it in an unrecognized state Commit: cd6c4d4db8bcb72ae931797c216b9829313850cf https://github.com/galaxyproject/galaxy/commit/cd6c4d4db8bcb72ae931797c216b… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-22 (Mon, 22 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Add job id to missing k8s log text Commit: c434c271598d95130439ac86c8b9060f42455e9a https://github.com/galaxyproject/galaxy/commit/c434c271598d95130439ac86c8b9… Author: Luca Pireddu <pireddu(a)gmail.com> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Improve k8s runner debug log message Commit: e235343f7674a5b74a707a693e94b80633d1ca2b https://github.com/galaxyproject/galaxy/commit/e235343f7674a5b74a707a693e94… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Push k8s log IOError handling into `__produce_log_file` Handling the IOError within the function should result in other call sites within the kubernets.py module properly setting the job state even if the job directory has been removed. Commit: cf02c9812759505d61f284d6d33ee9ce2dc994e8 https://github.com/galaxyproject/galaxy/commit/cf02c9812759505d61f284d6d33e… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Prefer `with open` syntax within kubernetes.py Commit: c13da94fd75d4b0010e4e3284649366c213a205d https://github.com/galaxyproject/galaxy/commit/c13da94fd75d4b0010e4e3284649… Author: Luca Pireddu <pireddu(a)crs4.it> Date: 2018-10-26 (Fri, 26 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Fix inverted log message arguments Thanks @pcm32! Commit: 1482cacee51a9fd91f65d54704c7bc36120f3a34 https://github.com/galaxyproject/galaxy/commit/1482cacee51a9fd91f65d54704c7… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/jobs/runners/kubernetes.py Log Message: ----------- Merge pull request #6886 from ilveroluca/fix/k8s_error_handling Improve k8s job error handling Commit: 49d9409f007dfe6288de4d6a2c0e15a4b45af022 https://github.com/galaxyproject/galaxy/commit/49d9409f007dfe6288de4d6a2c0e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Bam index is only available for coordinate sorted bam files Commit: 4c7ba6f0fe4a99c1324f70785d27b655ac8b5538 https://github.com/galaxyproject/galaxy/commit/4c7ba6f0fe4a99c1324f70785d27… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-10-30 (Tue, 30 Oct 2018) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #6946 from mvdbeek/bam_index_for_coordinate_sorted_only [18.09] Make Bam index only available for coordinate sorted bam files Commit: 717605af96bcb5fb9a5193295c9941d0d4632a93 https://github.com/galaxyproject/galaxy/commit/717605af96bcb5fb9a5193295c99… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M test/functional/tools/output_filter.xml Log Message: ----------- added test Commit: 20cecd2a68527015d8b98a430367b8fcdf9a364d https://github.com/galaxyproject/galaxy/commit/20cecd2a68527015d8b98a430367… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-10-31 (Wed, 31 Oct 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py Log Message: ----------- galaxy test needs to count data sets and collection outputs Commit: 30aaa296dd50471001323cc9895560219a33ce71 https://github.com/galaxyproject/galaxy/commit/30aaa296dd50471001323cc98955… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py A lib/galaxy/datatypes/test/1.qname_sorted.bam Log Message: ----------- Fix sniffing of readname sorted BAM files This fixes https://github.com/galaxyproject/galaxy/issues/6949. The problem is that `super` would fall back to the BamInputSorted sniffer, which prevents sniffing. Includes a test file for the new datatype upload testing framework. Commit: 4e098c5d5291209f4760010ff8bebd919ba19479 https://github.com/galaxyproject/galaxy/commit/4e098c5d5291209f4760010ff8be… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- tests: add parameter to output_filter Commit: 03eac8315d64e05df74f1f6fb286cff29e75f6b2 https://github.com/galaxyproject/galaxy/commit/03eac8315d64e05df74f1f6fb286… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix for workflow parameter collection in workflows view. Commit: 18644f91cf59265c1473d806845baffbf7a8132f https://github.com/galaxyproject/galaxy/commit/18644f91cf59265c1473d806845b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Avoid using var; let. Commit: 69b447169fb96048ea492a1d99d653585571c15b https://github.com/galaxyproject/galaxy/commit/69b447169fb96048ea492a1d99d6… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-01 (Thu, 01 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M lib/galaxy/datatypes/data.py Log Message: ----------- Allow deferring 'to_ext' extension to the server, implement for collections. Commit: 6b5f0a2ad1f21bbda92b06ff2700c961c34e84ea https://github.com/galaxyproject/galaxy/commit/6b5f0a2ad1f21bbda92b06ff2700… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Allow upload for ``rdata.sce`` format Commit: 6da5157181a085d183c099645216893fe512a1f9 https://github.com/galaxyproject/galaxy/commit/6da5157181a085d183c099645216… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge pull request #6963 from nsoranzo/release_18.05_allow_rdata.sce_upload [18.05] Allow upload for ``rdata.sce`` format Commit: 357e2f39c77026c81c56ed30ffae9f1905d2d82a https://github.com/galaxyproject/galaxy/commit/357e2f39c77026c81c56ed30ffae… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-11-02 (Fri, 02 Nov 2018) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Merge branch 'release_18.05' into release_18.09 Commit: 3d91738a697ff57047bc3cd505d5afc75de38f45 https://github.com/galaxyproject/galaxy/commit/3d91738a697ff57047bc3cd505d5… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-11-04 (Sun, 04 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #6955 from dannon/wf_param_fix [18.09] Fix for workflow parameter collection in workflows view. Commit: 3be8d66d71bcdb3eccde2d1a37731442ed1aa63a https://github.com/galaxyproject/galaxy/commit/3be8d66d71bcdb3eccde2d1a3773… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py Log Message: ----------- Remove unncecessary implementations of display_data These were not updated to use `_download_filename`, and so this fixes the download name for collection elements to include the element identifier. Note that the Data class should handle composite data just fine. Commit: f8b160535c5f9363e85c6c1d041b69ce5c3e9cc2 https://github.com/galaxyproject/galaxy/commit/f8b160535c5f9363e85c6c1d041b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/datatypes/blast.py Log Message: ----------- Some minor fixes for the blast datatype The signature for Data.display_data wasn't quite correct, and the description of display_data was also a little misleading. Commit: 9b42032098edaae076f5f88c48f135d8035a9ad6 https://github.com/galaxyproject/galaxy/commit/9b42032098edaae076f5f88c48f1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fill in default state for test_optional_workflow_output Commit: 2deb302ae7be93924a8bdcaff17a43caa0b5e3b4 https://github.com/galaxyproject/galaxy/commit/2deb302ae7be93924a8bdcaff17a… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M lib/galaxy/tools/verify/interactor.py M test/api/test_workflows.py M test/functional/tools/output_filter.xml Log Message: ----------- Merge pull request #6951 from bernt-matthias/topic/test-colouts-backport [18.09] Backport: tests need to count data sets and collections Commit: 61bda3d11a1d608ac8e1a731faf144ff989affc9 https://github.com/galaxyproject/galaxy/commit/61bda3d11a1d608ac8e1a731faf1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-11-05 (Mon, 05 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py Log Message: ----------- Merge pull request #6960 from dannon/collection_ext_dl [18.09] Allow deferring 'to_ext' extension to the server Commit: dbf5ef33604aae1a7294abf7bd5303504e8a4d2a https://github.com/galaxyproject/galaxy/commit/dbf5ef33604aae1a7294abf7bd53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Merge pull request #6974 from istevenshen/patch-2 Update locale.js Commit: fefa132cd741779a9c6a4bd03c44f473036a462a https://github.com/galaxyproject/galaxy/commit/fefa132cd741779a9c6a4bd03c44… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/workflow/workflow-view.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/blast.py M lib/galaxy/datatypes/data.py M lib/galaxy/datatypes/molecules.py M lib/galaxy/datatypes/neo4j.py A lib/galaxy/datatypes/test/1.qname_sorted.bam M lib/galaxy/jobs/runners/kubernetes.py M lib/galaxy/tools/verify/interactor.py M test/api/test_workflows.py M test/functional/tools/output_filter.xml Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.09' Compare: https://github.com/galaxyproject/galaxy/compare/315ca74305f1...fefa132cd741 **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] 5d3d8f: Update locale.js
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/release_18.09 Home: https://github.com/galaxyproject/galaxy Commit: 5d3d8f555901186bcbbd8885bb12da04ebc174a2 https://github.com/galaxyproject/galaxy/commit/5d3d8f555901186bcbbd8885bb12… Author: Steven Shen <ishenweiyan(a)qq.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Update locale.js Commit: dbf5ef33604aae1a7294abf7bd5303504e8a4d2a https://github.com/galaxyproject/galaxy/commit/dbf5ef33604aae1a7294abf7bd53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Merge pull request #6974 from istevenshen/patch-2 Update locale.js Compare: https://github.com/galaxyproject/galaxy/compare/61bda3d11a1d...dbf5ef33604a **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] 5d3d8f: Update locale.js
by GitHub 06 Nov '18

06 Nov '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 5d3d8f555901186bcbbd8885bb12da04ebc174a2 https://github.com/galaxyproject/galaxy/commit/5d3d8f555901186bcbbd8885bb12… Author: Steven Shen <ishenweiyan(a)qq.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Update locale.js Commit: 315ca74305f10c88c21bfc5b58805c698c0a5737 https://github.com/galaxyproject/galaxy/commit/315ca74305f10c88c21bfc5b5880… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-11-06 (Tue, 06 Nov 2018) Changed paths: M client/galaxy/scripts/nls/zh/locale.js Log Message: ----------- Merge pull request #6974 from istevenshen/patch-2 Update locale.js Compare: https://github.com/galaxyproject/galaxy/compare/cea9521b1a01...315ca74305f1 **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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