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

[galaxyproject/infrastructure-playbook] 07740c: Increase Jetstream @ IU large node count to 12
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 07740ce4947bdede98d57f0a895e52d7bd84f109 https://github.com/galaxyproject/infrastructure-playbook/commit/07740ce4947… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/jsiu/templates/slurm/slurm.conf.j2 Log Message: ----------- Increase Jetstream @ IU large node count to 12 Commit: 1032dfe139edaae4881c13e50303e6cf7e6b71c3 https://github.com/galaxyproject/infrastructure-playbook/commit/1032dfe139e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/jsiu/templates/slurm/slurm.conf.j2 Log Message: ----------- Increase Jetstream @ IU node counts Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/03c145db56… **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] 03c145: Use synchronize instead of slow file/copy
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 03c145db560ff8f213f76afff06fa9716e8ffe19 https://github.com/galaxyproject/infrastructure-playbook/commit/03c145db560… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M roles/slurmscale/files/roles/galaxynodeconfig/tasks/main.yml M roles/slurmscale/tasks/main.yml Log Message: ----------- Use synchronize instead of slow file/copy Also fix CVMFS cache size setting **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 15ce8c: Update Test
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 15ce8c98ba3c1d1b88f69a3e2d0bf65414cb04c5 https://github.com/galaxyproject/usegalaxy-playbook/commit/15ce8c98ba3c1d1b… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/test/files/galaxy/galaxy_version.yml Log Message: ----------- Update Test **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/infrastructure-playbook] fef2c3: Make galaxy-db-02 a CVMFS client
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: fef2c391de172dbdbcba93ce14811c47cc35e1c0 https://github.com/galaxyproject/infrastructure-playbook/commit/fef2c391de1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/tacc/inventory Log Message: ----------- Make galaxy-db-02 a CVMFS client **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 2b8b4e: grt - wrap every write in try-except
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b8b4e198d4f4f498284017d1c9696cbec5f7cf0 https://github.com/galaxyproject/galaxy/commit/2b8b4e198d4f4f498284017d1c96… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- grt - wrap every write in try-except and just fail the row if the data is crap (like {NULL, SOH, STX, ETX} and friends) Commit: f21c8caf83f6b511de6bd5b78e1aa75326823c47 https://github.com/galaxyproject/galaxy/commit/f21c8caf83f6b511de6bd5b78e1a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- unname the exception Commit: bde05ac88b66af597e9243d68b7ae8bb364e7653 https://github.com/galaxyproject/galaxy/commit/bde05ac88b66af597e9243d68b7a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6354 from martenson/superdefensive-grt [18.05] grt - wrap every write in try-except Commit: 69c8ce7e92ff41341dff855df3149ae90ca619ed https://github.com/galaxyproject/galaxy/commit/69c8ce7e92ff41341dff855df314… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Fix size handling in legacy modal view Commit: 9f4926bd9a4f35040126cfcaa6a41c7024c3035a https://github.com/galaxyproject/galaxy/commit/9f4926bd9a4f35040126cfcaa6a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Limit modal body size to 67 percent of window height Commit: f6888a32d68d4f1be0b09257a390754a85319da3 https://github.com/galaxyproject/galaxy/commit/f6888a32d68d4f1be0b09257a390… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Add fasta datatype to msa viewer Commit: b0212ff45cf0bc6964278aac49cc42b0ebebdb65 https://github.com/galaxyproject/galaxy/commit/b0212ff45cf0bc6964278aac49cc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Add phylip for msa viewer Commit: 817d043f123563c77e8b430f95d347bbd482d49e https://github.com/galaxyproject/galaxy/commit/817d043f123563c77e8b430f95d3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Merge pull request #6361 from guerler/fix_msa [18.05] Add fasta datatype to msa viewer Commit: c601a9d4915388196dc7b00d9cc4090af2b95937 https://github.com/galaxyproject/galaxy/commit/c601a9d4915388196dc7b00d9cc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py Log Message: ----------- Fix collection mapping to allow mapping over multi-data inputs. It is jarring to users that works for collection inputs but not multiple data inputs, especially because the IUC discourages collection inputs when multiple data inputs would work. Commit: 6b8b862e4d0d6195fb85f4c91419e115dd5564ee https://github.com/galaxyproject/galaxy/commit/6b8b862e4d0d6195fb85f4c91419… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix up subcollection_type Commit: 6b7ee55bac71859c26936a7a154dad6e090047d3 https://github.com/galaxyproject/galaxy/commit/6b7ee55bac71859c26936a7a154d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Test list collection mapping over multidata input Commit: 9e3de244d7184d059e7d19cce01386e99ad85f14 https://github.com/galaxyproject/galaxy/commit/9e3de244d7184d059e7d19cce013… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix mapping list over multidata input Commit: 7cfbb032f61bbaf77be198117ba8eaa4b081c094 https://github.com/galaxyproject/galaxy/commit/7cfbb032f61bbaf77be198117ba8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/functional/tools/for_workflows/cat_collection.xml Log Message: ----------- Break test by adding "list" to collection_type This will break tests trying to map over list:pair collections, for instance test_extract_workflows_with_dataset_collections. Commit: b53d2ae3817f2c58f5e1b9f0763ee7b16cc13b81 https://github.com/galaxyproject/galaxy/commit/b53d2ae3817f2c58f5e1b9f0763e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py Log Message: ----------- Fix can_map_over for mapping over paired inputs We'd only try mapping over the first collection type description otherwise. I suppose we didn't notice because the first type is `list` and therefore much more common. Noticed this while working on https://github.com/galaxyproject/galaxy/pull/5640. Commit: f5aec1cdf18d44d4f3dc74811f421f346fc3c0f7 https://github.com/galaxyproject/galaxy/commit/f5aec1cdf18d44d4f3dc74811f42… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py Log Message: ----------- Fix inferring output structure when mapping over Previously this would have always generated `list:list` structures, even when the input is a list:pair. I'm not 100% convinced this is correct, but this seems to work. Commit: 647ba8531acdf576cfefea71bc7bb73a89ed7a0a https://github.com/galaxyproject/galaxy/commit/647ba8531acdf576cfefea71bc7b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test tool and workflow for mapping over with mapping output This doesn't quite work because of the dynamic output collection, which fails with: ``` galaxy.tools.parameters.output_collect DEBUG 2018-06-06 18:40:38,784 (3) Add dynamic collection datasets to history for output [reverse] (171.970 ms) galaxy.tools.parameters.output_collect ERROR 2018-06-06 18:40:38,839 Problem gathering output collection. Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 340, in collect_dynamic_outputs collection_builder.populate() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 88, in populate elements = self.build_elements() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 59, in build_elements new_elements[identifier] = element.build() AttributeError: 'HistoryDatasetAssociation' object has no attribute 'build' ``` This seems to happen because the inner collection is wrongly detected as nested. In general I doubt that mapping over colleciton output works with dynamically discovered output collections. Commit: 5e32d78aa7daba492ce31577481f983bd1580b68 https://github.com/galaxyproject/galaxy/commit/5e32d78aa7daba492ce31577481f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Consider mapping-over when picking collection_type for dynamically discovered collections Commit: 333d660556129b66f0bb9e3a117f9003a4bfb368 https://github.com/galaxyproject/galaxy/commit/333d660556129b66f0bb9e3a117f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Recover the correct DataCollectionToolParameter when checking if a collection is being mapped over Commit: 128a1731e42c5eb4cdf7edf939f7a5c5b3eddbc7 https://github.com/galaxyproject/galaxy/commit/128a1731e42c5eb4cdf7edf939f7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Merge pull request #6360 from guerler/legacy_modal_scrolling [18.05] Fix size handling in legacy modal view Commit: b8536c2005c69c42b20509b770f3888a5cbc80e8 https://github.com/galaxyproject/galaxy/commit/b8536c2005c69c42b20509b770f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/for_workflows/cat_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'jmchilton/collection_fixes' into release_18.05 Commit: bcf105cbb37a1c16b2109192c1271b2f4d5847d8 https://github.com/galaxyproject/galaxy/commit/bcf105cbb37a1c16b2109192c127… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/layout/modal.js M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Client build. Commit: f9ba72f0aecbb4cdf50a0444dcbec72cc7b8569c https://github.com/galaxyproject/galaxy/commit/f9ba72f0aecbb4cdf50a0444dcbe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js M config/plugins/visualizations/msa/config/msa.xml M scripts/grt/export.py Log Message: ----------- Merge remote-tracking branch 'upstream/release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/1c7387c53a0b...f9ba72f0aecb **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f7ffde: Alias btn-xs to btn-sm for thinks (like welcome) w...
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: f7ffde9db447be807f3c7924bbfe243c3f6faa51 https://github.com/galaxyproject/galaxy/commit/f7ffde9db447be807f3c7924bbfe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Alias btn-xs to btn-sm for thinks (like welcome) which may have been customized and rely on the previous styles. Commit: db444455b29b008b0f3bdf0844f38a4db1e457ef https://github.com/galaxyproject/galaxy/commit/db444455b29b008b0f3bdf0844f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Alias btn-default to btn-secondary for backwards compatibility. Commit: 074ec18490e2fb86c17a506374d78269c29ae03f https://github.com/galaxyproject/galaxy/commit/074ec18490e2fb86c17a506374d7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tours.js M static/style/blue/base.css Log Message: ----------- Missed label->badge translations. Commit: 69c74d52d4a4614aa544abd2c7a810fa817b7404 https://github.com/galaxyproject/galaxy/commit/69c74d52d4a4614aa544abd2c7a8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-25 (Fri, 25 May 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tours.js M static/style/blue/base.css Log Message: ----------- Drop sm-badge-pad completely (standard styles handle this now) Commit: 2ad4dde0729bbce690f744730b4b2f2af39b1fef https://github.com/galaxyproject/galaxy/commit/2ad4dde0729bbce690f744730b4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Convert history-contents urlroot to instance var Commit: 46290939092a8068836712176ddbfc7641f69ada https://github.com/galaxyproject/galaxy/commit/46290939092a8068836712176ddb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix history list bottom border Commit: 7e220205f38abbe6d44f93f5ccfb14506838118a https://github.com/galaxyproject/galaxy/commit/7e220205f38abbe6d44f93f5ccfb… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/history.scss Log Message: ----------- A more accurate version of what was set before, with the same outcome (though, it could change if we toggle the grey) Commit: cf3ed04d742938de52c24386dcf2f0c10409df71 https://github.com/galaxyproject/galaxy/commit/cf3ed04d742938de52c24386dcf2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix dataset messagesmall display, was a TODO left from migration Commit: 6cf4c8e5f4780421dc45472bf495694dd49aaa47 https://github.com/galaxyproject/galaxy/commit/6cf4c8e5f4780421dc45472bf495… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/history.scss M static/style/blue/base.css Log Message: ----------- Fix one more busted fade Commit: 77dff21bcc6c1b2f93d400307a7f3332772f9943 https://github.com/galaxyproject/galaxy/commit/77dff21bcc6c1b2f93d400307a7f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Fix (ancient, should replace this, but might as well make it work until we do) tool-shed-only grid search button Commit: 361b48a4d22e0f61ac6dcdf0d306d17d89b9d166 https://github.com/galaxyproject/galaxy/commit/361b48a4d22e0f61ac6dcdf0d306… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako Log Message: ----------- Drop submit-image custom styling, use standard fa; left it as inline style to keep it clean and remove all at once when this grid goes. Commit: 9fe40db5b3cf82f09ae3a783a8b708e78239f27f https://github.com/galaxyproject/galaxy/commit/9fe40db5b3cf82f09ae3a783a8b7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/list-item.scss M static/style/blue/base.css Log Message: ----------- Fix list panel control message margins. Commit: 0e39cf1924cfacb879802934da0112470cba9a0e https://github.com/galaxyproject/galaxy/commit/0e39cf1924cfacb879802934da01… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/style/scss/upload.scss Log Message: ----------- This is correct now Commit: 18ae4457a131948fe87b7038215e81dec647e3db https://github.com/galaxyproject/galaxy/commit/18ae4457a131948fe87b7038215e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-29 (Tue, 29 May 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss Log Message: ----------- Formatting for styles and a couple misc files Commit: f35c1d6630961f6ae5e9393ebd1504831765bcf8 https://github.com/galaxyproject/galaxy/commit/f35c1d6630961f6ae5e9393ebd15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-30 (Wed, 30 May 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Overhaul workflow execution response, including appropriate text for new histories, and multiple executions. With links. Commit: c0c8aad528d9164fb7aaf88c3a202c66044c0134 https://github.com/galaxyproject/galaxy/commit/c0c8aad528d9164fb7aaf88c3a20… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Fix history shared with me 'view' link Commit: 692465d4ec9a4493ae1326cbc8b118cf49f5cbff https://github.com/galaxyproject/galaxy/commit/692465d4ec9a4493ae1326cbc8b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Standard quotes. Commit: 8a0427a6e8eeffde3022ed1187b114265b73447f https://github.com/galaxyproject/galaxy/commit/8a0427a6e8eeffde3022ed1187b1… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #6257 from dannon/sharing_link_fix [18.05] Fix history shared with me 'view' link Commit: 87dc52cd8fedf64e895d0aa8421207f52a390e01 https://github.com/galaxyproject/galaxy/commit/87dc52cd8fedf64e895d0aa84212… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-05-31 (Thu, 31 May 2018) Changed paths: M client/galaxy/scripts/components/HistoryView.vue Log Message: ----------- Only show 'switch to this history' when the person in question is the history owner. Commit: 6dee708ae8cdad5ccc9f7ae095dae736b44a6091 https://github.com/galaxyproject/galaxy/commit/6dee708ae8cdad5ccc9f7ae095da… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- export another tsv file named datasets.tsv Commit: 11575132dc4fba88751a5e2228956dfc1b75bbe2 https://github.com/galaxyproject/galaxy/commit/11575132dc4fba88751a5e222895… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-01 (Fri, 01 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- exports a dataset tsv Commit: 0ea8107191ea1a3bc8b4b57623c981c06f38092e https://github.com/galaxyproject/galaxy/commit/0ea8107191ea1a3bc8b4b57623c9… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh Log Message: ----------- Use separate `pid_log_paster_args` variable to store --pid-file and --log-file options of `./scripts/paster.py` . https://github.com/galaxyproject/galaxy/pull/6239 fixed 3 bugs: - `GALAXY_RUN_ALL=1 ./run.sh` was reusing the same pid and log files for all Galaxy processes; - `./run.sh restart` was always using `paster.pid` and `paster.log` instead of the configured files - `./run.sh status` was always using `paster.pid` but also introduced a regression, i.e. the plain `./run.sh` started writing to the log file instead of the standard output (console). This fixes the regression by using a separate variable for these options instead of conflating them in `paster_args` or `server_args`. Commit: 87719b9f8edaa983ea70e48532367547d6b2ffdb https://github.com/galaxyproject/galaxy/commit/87719b9f8edaa983ea70e4853236… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M run.sh Log Message: ----------- Check for empty pid file when using --wait Fix this error message: ``` Executing: python ./scripts/paster.py serve config/galaxy.ini --daemon --server-name="main" --pid-file="main.pid" --log-file="main.log" Entering daemon mode ../run.sh: 96: [: Illegal number: ..... ``` Commit: c9daa60e91392c7e7e55fde4af38d0a067fc4fb8 https://github.com/galaxyproject/galaxy/commit/c9daa60e91392c7e7e55fde4af38… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M scripts/common_startup.sh Log Message: ----------- Look for config file inside galaxy.dependencies.optional() Also don't fail if no config file is found, just print a message on stderr. This allows the removal of the code to set `GALAXY_CONFIG_FILE` from `scripts/common_startup.sh` . Commit: aaff4741422ba4442021a47773c7b1824b98a4e6 https://github.com/galaxyproject/galaxy/commit/aaff4741422ba4442021a47773c7… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-02 (Sat, 02 Jun 2018) Changed paths: M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh M scripts/maintenance.sh Log Message: ----------- Use consistent preference order for config files 1) galaxy.yml 2) galaxy.ini 3) universe_wsgi.ini Also: - properly quote variables which may contain spaces - no need to pass the config file to `./scripts/manage_tool_dependencies.py` - simplify `scripts/maintenance.sh` by moving the `cd` up and reusing functions from `scripts/common_startup_functions.sh` Commit: 49a1be4f1de3cfe48bbfd0b709bc8a158f7d36e6 https://github.com/galaxyproject/galaxy/commit/49a1be4f1de3cfe48bbfd0b709bc… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/tools/parser/output_actions.py Log Message: ----------- Allow from_param to reference a child collection This is necessary when mapping over a collection over an input that is referenced in the output section, like so: ``` ... <when value="paired_collection"> <action type="format"> <option type="from_param" name="library.input_1" param_attribute="reverse.ext" /> </action> </when> ... ``` Commit: bc8254faecf9b9f9bbd000d9ba7601ce9fe472a5 https://github.com/galaxyproject/galaxy/commit/bc8254faecf9b9f9bbd000d9ba76… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py Log Message: ----------- Do not adapt target collection to child collection type Otherwise mapping over list:list:pair to a pair input breaks at https://github.com/galaxyproject/galaxy/blob/21b44bf348ae10d170ab96a3b6f30b…. This and the previous commit should fix https://github.com/galaxyproject/tools-iuc/issues/1563. Commit: 3e22b0b11b600a4e957557d3cece03665bdc7de5 https://github.com/galaxyproject/galaxy/commit/3e22b0b11b600a4e957557d3cece… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Test case for mapping over inputs with output ftype determined via input extension Commit: aa062f8546379bd35769314fb3470fde02445157 https://github.com/galaxyproject/galaxy/commit/aa062f8546379bd35769314fb347… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- fixed the issues with the last pull Commit: 0c852257bb9f91983a4afe063bf8d64692802e87 https://github.com/galaxyproject/galaxy/commit/0c852257bb9f91983a4afe063bf8… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- delete comment thats no longer necessary Commit: 5b7055fc6f19e2a0489a92bb8f4762a1b6a1ece1 https://github.com/galaxyproject/galaxy/commit/5b7055fc6f19e2a0489a92bb8f47… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- respect blacklisted tools Commit: 4630994fd0479e66357315fc7e2fa2c20367fb84 https://github.com/galaxyproject/galaxy/commit/4630994fd0479e66357315fc7e2f… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- get output datasets as well Commit: ba45c15fffcb9e54dda35759410675d78346394f https://github.com/galaxyproject/galaxy/commit/ba45c15fffcb9e54dda357594106… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- tried to fix some of stylization fails Commit: 948d0767eb9b2e2a6207ead2456a6580e34eaf84 https://github.com/galaxyproject/galaxy/commit/948d0767eb9b2e2a6207ead2456a… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- more style fixes Commit: 191a134bbc511c508d9ee0636030da2e2e68ea44 https://github.com/galaxyproject/galaxy/commit/191a134bbc511c508d9ee0636030… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- got rid of things that are no longer necessary Commit: 6db9fd3d51b91804e24ed393468973ecfb659eef https://github.com/galaxyproject/galaxy/commit/6db9fd3d51b91804e24ed3934689… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- style fix Commit: dd4de3f3b28f1ddd92aaa87c4f2c00657ecbc457 https://github.com/galaxyproject/galaxy/commit/dd4de3f3b28f1ddd92aaa87c4f2c… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- catch dataset_id=None Commit: c37e3844543b1bd425cfd370830bdb235674706f https://github.com/galaxyproject/galaxy/commit/c37e3844543b1bd425cfd370830b… Author: Anastasia Tyryshkina <atyryshkina(a)gmail.com> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- style fix Commit: a40abcd6e42e62a7e46e0afa71c04c152ee8db4a https://github.com/galaxyproject/galaxy/commit/a40abcd6e42e62a7e46e0afa71c0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6263 from atyryshkina/modify-grt-export [18.05] Fix dataset sizes in GRT export script Commit: b62099f4188f5dcdfe9fc955cdd3059a22b76d38 https://github.com/galaxyproject/galaxy/commit/b62099f4188f5dcdfe9fc955cdd3… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- change to a more defensive approach, clarify varnames Commit: e767438afc305b1c426c7c9152a58bd54b7c1f8e https://github.com/galaxyproject/galaxy/commit/e767438afc305b1c426c7c9152a5… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-05 (Tue, 05 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- add spaces before inline comment Commit: 5a0f98802cab73dfcdaef01b1200e96bc6b9a8ae https://github.com/galaxyproject/galaxy/commit/5a0f98802cab73dfcdaef01b1200… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Strip a spurious Slurm warning from job stderr Reason for the Slurm warning ---------------------------- The Linux kernel memory controller (responsible for the memory cgroup) may run out of cgroup subsystem state (CSS) IDs. When a cgroup is created it is assigned a CSS ID to manage its state. Upon removal of the cgroup the corresponding state information (e.g. cache entries) may still exist and therefore the CSS ID is still held. When multiple frequent short-lived jobs are run on a cluster node, the number of available CSS IDs becomes exhausted and creating a new memory cgroup results in a ENOSPC ("No space left on device"), which is reported by SLURM with the message "unable to add task[pid=<PID>] to memory cg '(null)'" (even if jobs run fine). There is a bugfix for the kernel that releases the CSS ID upon cgroup destruction, but it appears to be only available after Linux 4.4. We use CentOS 7, which is based on Linux 3.10. The only temporary solutions is to reboot the affected cluster node. Thanks to @tuxtobin for the detailed analysis above. Reason for this patch --------------------- Many tools rely on an empty stderr to determine if the job was successful, either because they were never updated to use `<stdio>`/`detect_errors`, or because the underlying tool returns a non-zero exit code when successful, e.g. `tranalign` from https://toolshed.g2.bx.psu.edu/view/devteam/emboss_5/832c20329690 . Even using a `<regex>` inside `<stdio>` would not work because the Slurm warning contains the word `error`. Commit: a0004db7203edd6c0a22fc35658fb1f018665a83 https://github.com/galaxyproject/galaxy/commit/a0004db7203edd6c0a22fc35658f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh M scripts/maintenance.sh Log Message: ----------- Merge pull request #6262 from nsoranzo/release_18.01_fix_run_scripts [18.01] Various fixes for the run scripts Commit: 2b8beb69c4ff5ed393026fa8864940e9629369c5 https://github.com/galaxyproject/galaxy/commit/2b8beb69c4ff5ed393026fa88649… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dependencies/__init__.py M run.sh M run_reports.sh M run_tool_shed.sh M scripts/common_startup.sh M scripts/common_startup_functions.sh R scripts/common_startup_variables.sh M scripts/maintenance.sh Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: acb4cdf5843abbfb110b6cc00e6cb1e1acdfac95 https://github.com/galaxyproject/galaxy/commit/acb4cdf5843abbfb110b6cc00e6c… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6285 from martenson/grt-defensive [18.05] telescope export: change to a more defensive approach Commit: 7b741a32cddb94442c7663f94c6c3b29e91e4158 https://github.com/galaxyproject/galaxy/commit/7b741a32cddb94442c7663f94c6c… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Broken in commit 0ea8107191ea1a3bc8b4b57623c981c06f38092e . Reported by @lparsons in https://github.com/galaxyproject/galaxy/pull/6262#issuecomment-395113621 Commit: a2fe4b0c76fa9cfff9e974b76e4d5ea34679a881 https://github.com/galaxyproject/galaxy/commit/a2fe4b0c76fa9cfff9e974b76e4d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M run.sh Log Message: ----------- Merge pull request #6295 from nsoranzo/release_18.01_followup_on_6262 [18.01] Fix `GALAXY_RUN_ALL=1 ./run.sh --daemon` Commit: 3007c93d7c5bf6ccb7c6b8d5df95ebdf60ac4a8b https://github.com/galaxyproject/galaxy/commit/3007c93d7c5bf6ccb7c6b8d5df95… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #6266 from jmchilton/from_param_fixes_backport [18.01] Backport fixes for collection output actions. Commit: 711070dc4c18af7a2da2a2a8bcafb4112efb0daf https://github.com/galaxyproject/galaxy/commit/711070dc4c18af7a2da2a2a8bcaf… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/subcollections.py M lib/galaxy/tools/parser/output_actions.py M run.sh M test/api/test_tools.py A test/functional/tools/output_action_change_format_paired.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: ed56454ca07f3e07ce2bfced8614ca3dc560649a https://github.com/galaxyproject/galaxy/commit/ed56454ca07f3e07ce2bfced8614… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M scripts/grt/grt.yml.sample Log Message: ----------- add the canonical url to grt config Commit: 36fcb5c1b74f7b7b84827311133957eb7249b277 https://github.com/galaxyproject/galaxy/commit/36fcb5c1b74f7b7b848273111339… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-07 (Thu, 07 Jun 2018) Changed paths: M scripts/grt/grt.yml.sample Log Message: ----------- Merge pull request #6301 from martenson/grt-config [18.05] add the canonical url to grt config Commit: 753ecd625c1410a3a6dc2c4a30e3f81fb71be29e https://github.com/galaxyproject/galaxy/commit/753ecd625c1410a3a6dc2c4a30e3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Increase sleep if encountering exception Commit: 12f51a47897faf55461626a504b61fa2793777d6 https://github.com/galaxyproject/galaxy/commit/12f51a47897faf55461626a504b6… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M lib/galaxy/jobs/handler.py Log Message: ----------- Merge pull request #6304 from mvdbeek/sleep_more [18.05] Increase sleep if encountering (DB locking) exception Commit: f1adf0a7920720ea7f20cdc3a21ea014f9ddd699 https://github.com/galaxyproject/galaxy/commit/f1adf0a7920720ea7f20cdc3a21e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/job-states-model.js M client/galaxy/style/scss/base.scss M client/galaxy/style/scss/history.scss M client/galaxy/style/scss/list-item.scss M client/galaxy/style/scss/upload.scss M static/style/blue/base.css M templates/webapps/tool_shed/common/grid_common.mako Log Message: ----------- Merge pull request #6238 from dannon/1805stylefixes_rebased [18.05] Various style fixes for history, toolshed, messages (backport) Commit: 75c9610fdaf1a59806e75458e04f1319e95f5a40 https://github.com/galaxyproject/galaxy/commit/75c9610fdaf1a59806e75458e04f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #6243 from dannon/workflow_submit_text_backport [18.05] Backport of Workflow Execution Text Fixup Commit: 20cf8b5bf0f4632d0f3c275c3261f920bbf76211 https://github.com/galaxyproject/galaxy/commit/20cf8b5bf0f4632d0f3c275c3261… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/tours.js M static/style/blue/base.css Log Message: ----------- Merge pull request #6226 from dannon/minor_style_fixes [18.05] Two minor aliases for (exterior) backwards compatibility, minor badge tweaks Commit: 54ec854c130f92f49d2c3f42e2e8971d6676a79a https://github.com/galaxyproject/galaxy/commit/54ec854c130f92f49d2c3f42e2e8… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- remove outdated comment Commit: 85265ebd793a43d8df048e613cdfb4578f4f6e18 https://github.com/galaxyproject/galaxy/commit/85265ebd793a43d8df048e613cdf… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js Log Message: ----------- Merge pull request #6237 from dannon/history_contents_multiview [18.05] Fix history contents w/ proxy prefix (multiview error) Commit: a56c4e9cf6b929e43dd2dcb6891bd54706e21025 https://github.com/galaxyproject/galaxy/commit/a56c4e9cf6b929e43dd2dcb6891b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/components/HistoryView.vue Log Message: ----------- Merge pull request #6260 from dannon/history-view-fixes [18.05] History view 'import' button display based on ownership. Commit: 7eb927b631a3677a74b055fc275b90827bcdff21 https://github.com/galaxyproject/galaxy/commit/7eb927b631a3677a74b055fc275b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/hdca-li-edit.js Log Message: ----------- Fix delete "Collection Only" option in history menu. Broken with https://github.com/galaxyproject/galaxy/commit/7cc01380afd017c5cac2af2b2d73…. Commit: 9957c027375c436b64299240982a2165d83b7ff3 https://github.com/galaxyproject/galaxy/commit/9957c027375c436b64299240982a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue Log Message: ----------- Fix file type error in RuleCollectionBuilder. Commit: 3c36bec2903e6c012428912c424f4ad762d1b96a https://github.com/galaxyproject/galaxy/commit/3c36bec2903e6c012428912c424f… Author: Sebastian Kapust <sebastian(a)kapust.org> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M config/plugins/webhooks/demo/search/script.js Log Message: ----------- Fix tool search overlay link Commit: 96fbe9702dc07eb965a6e6ede3db8e9df91f8e19 https://github.com/galaxyproject/galaxy/commit/96fbe9702dc07eb965a6e6ede3db… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- backport and build client Commit: dba21dc8a42640b679d1076bb7f8089028aa31fa https://github.com/galaxyproject/galaxy/commit/dba21dc8a42640b679d1076bb7f8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-08 (Fri, 08 Jun 2018) Changed paths: M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/mvc/history/hdca-li-edit.js M config/plugins/webhooks/demo/search/script.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/libs.bundled.js M static/scripts/mvc/history/hdca-li-edit.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/tool/tool-form-composite.js Log Message: ----------- Merge pull request #6311 from martenson/backport-and-build [18.05] Backport and build client changes Commit: e7b7bee82e60acea478db2dbf2cc03552ebf6cd4 https://github.com/galaxyproject/galaxy/commit/e7b7bee82e60acea478db2dbf2cc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/jobs/runners/slurm.py Log Message: ----------- Merge pull request #6293 from nsoranzo/release_18.05_strip_slurm_warning [18.05] Strip a spurious Slurm warning from job stderr Commit: 3a17db8f205f57902b35b2245c8367802beb5faa https://github.com/galaxyproject/galaxy/commit/3a17db8f205f57902b35b2245c83… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-14 (Thu, 14 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js Log Message: ----------- Backbone model url fixes (urlRoot isn't necessary in many of these situations, and only complicates (and breaks) some things Convert history-contents urlroot to instance var remove outdated comment Commit: 2e7dd84583dd3f138346cf6c930fe82011da2fd7 https://github.com/galaxyproject/galaxy/commit/2e7dd84583dd3f138346cf6c930f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-14 (Thu, 14 Jun 2018) Changed paths: M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js Log Message: ----------- Rebuild client w/ maps. Commit: c2307f3f1aae8f46fd1023accdf0a6c1c435eba3 https://github.com/galaxyproject/galaxy/commit/c2307f3f1aae8f46fd1023accdf0… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- added missing level fatal_oom to xsd Commit: 8d75a67386f72814c17ad1abef5d0154b247a521 https://github.com/galaxyproject/galaxy/commit/8d75a67386f72814c17ad1abef5d… Author: M Bernt <m.bernt(a)ufz.de> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- also added missing documentation Commit: fc47618f6798d48f3ab903a8ea6231067bf0fed2 https://github.com/galaxyproject/galaxy/commit/fc47618f6798d48f3ab903a8ea62… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: A scripts/plugin_staging.py Log Message: ----------- Initial python-based plugin staging. to be used from common startup. Commit: e110489cc55f25b7d5ec7b9e5cbc5d914215b806 https://github.com/galaxyproject/galaxy/commit/e110489cc55f25b7d5ec7b9e5cbc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/common_startup.sh Log Message: ----------- Call plugin static dir regeneration in the event client isn't being built (which also does this, albeit slightly differently) Commit: 9ac0161891a92db7a359e13a74e831ec17a79317 https://github.com/galaxyproject/galaxy/commit/9ac0161891a92db7a359e13a74e8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Update description for installing pbs-python Commit: 370ea25d2c58b7e55f6bc062062e9a962a08ea7d https://github.com/galaxyproject/galaxy/commit/370ea25d2c58b7e55f6bc062062e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Minor refactoring, comments. Commit: 8364ebebcd81b6f8bf6c1122e5271a5c5eb23868 https://github.com/galaxyproject/galaxy/commit/8364ebebcd81b6f8bf6c1122e527… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/get_uwsgi_args.py Log Message: ----------- Add static-safe mapping for uwsgi for plugin static dirs, which are accessible via symlink Commit: 4cdd210bb27cd1c271e69c8dfd46585f0c232ef9 https://github.com/galaxyproject/galaxy/commit/4cdd210bb27cd1c271e69c8dfd46… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/plugin_staging.py Log Message: ----------- Use os.pardir instead of ../. Thanks @nsoranzo Commit: 37ad1a8bdce963b4152331685e3755a60777e633 https://github.com/galaxyproject/galaxy/commit/37ad1a8bdce963b4152331685e37… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge pull request #6345 from mvdbeek/update_pbs_python_doc [18.01] Update description for installing pbs-python Commit: cddee94e4bb043381433030e34f3f9129382830f https://github.com/galaxyproject/galaxy/commit/cddee94e4bb043381433030e34f3… Author: Nicola Soranzo <nicola.soranzo(a)gmail.com> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Small fixes Commit: 12a05c782099da0eb846069fe96355fb50212fef https://github.com/galaxyproject/galaxy/commit/12a05c782099da0eb846069fe963… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-15 (Fri, 15 Jun 2018) Changed paths: M scripts/common_startup.sh M scripts/get_uwsgi_args.py A scripts/plugin_staging.py Log Message: ----------- Merge pull request #6344 from dannon/python_static_staging [18.05] Visualization static staging Commit: a2ff5efbce3023b12a774600b331867d7320898a https://github.com/galaxyproject/galaxy/commit/a2ff5efbce3023b12a774600b331… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-16 (Sat, 16 Jun 2018) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Merge pull request #6341 from bernt-matthias/release_18.05_fix_xsd [18.05] Added missing level fatal_oom to xsd Commit: 3707fb4eb1287a95edf8532c9c7856a3b7560d9f https://github.com/galaxyproject/galaxy/commit/3707fb4eb1287a95edf8532c9c78… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2018-06-17 (Sun, 17 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/extended.bundled.js M static/scripts/bundled/extended.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js Log Message: ----------- Merge pull request #6336 from dannon/backport_url_fix_flattened [18.01] Backport backbone url fixes (flattened) Commit: e8beea0d60c1a4b88b67cc3f176e11ae76215f67 https://github.com/galaxyproject/galaxy/commit/e8beea0d60c1a4b88b67cc3f176e… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-17 (Sun, 17 Jun 2018) Changed paths: M doc/source/admin/cluster.md Log Message: ----------- Merge branch 'release_18.01' into release_18.05 Commit: 2b8b4e198d4f4f498284017d1c9696cbec5f7cf0 https://github.com/galaxyproject/galaxy/commit/2b8b4e198d4f4f498284017d1c96… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- grt - wrap every write in try-except and just fail the row if the data is crap (like {NULL, SOH, STX, ETX} and friends) Commit: f21c8caf83f6b511de6bd5b78e1aa75326823c47 https://github.com/galaxyproject/galaxy/commit/f21c8caf83f6b511de6bd5b78e1a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- unname the exception Commit: bde05ac88b66af597e9243d68b7ae8bb364e7653 https://github.com/galaxyproject/galaxy/commit/bde05ac88b66af597e9243d68b7a… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-18 (Mon, 18 Jun 2018) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge pull request #6354 from martenson/superdefensive-grt [18.05] grt - wrap every write in try-except Commit: 69c8ce7e92ff41341dff855df3149ae90ca619ed https://github.com/galaxyproject/galaxy/commit/69c8ce7e92ff41341dff855df314… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Fix size handling in legacy modal view Commit: 9f4926bd9a4f35040126cfcaa6a41c7024c3035a https://github.com/galaxyproject/galaxy/commit/9f4926bd9a4f35040126cfcaa6a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Limit modal body size to 67 percent of window height Commit: f6888a32d68d4f1be0b09257a390754a85319da3 https://github.com/galaxyproject/galaxy/commit/f6888a32d68d4f1be0b09257a390… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Add fasta datatype to msa viewer Commit: b0212ff45cf0bc6964278aac49cc42b0ebebdb65 https://github.com/galaxyproject/galaxy/commit/b0212ff45cf0bc6964278aac49cc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Add phylip for msa viewer Commit: 817d043f123563c77e8b430f95d347bbd482d49e https://github.com/galaxyproject/galaxy/commit/817d043f123563c77e8b430f95d3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Merge pull request #6361 from guerler/fix_msa [18.05] Add fasta datatype to msa viewer Commit: c601a9d4915388196dc7b00d9cc4090af2b95937 https://github.com/galaxyproject/galaxy/commit/c601a9d4915388196dc7b00d9cc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py Log Message: ----------- Fix collection mapping to allow mapping over multi-data inputs. It is jarring to users that works for collection inputs but not multiple data inputs, especially because the IUC discourages collection inputs when multiple data inputs would work. Commit: 6b8b862e4d0d6195fb85f4c91419e115dd5564ee https://github.com/galaxyproject/galaxy/commit/6b8b862e4d0d6195fb85f4c91419… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix up subcollection_type Commit: 6b7ee55bac71859c26936a7a154dad6e090047d3 https://github.com/galaxyproject/galaxy/commit/6b7ee55bac71859c26936a7a154d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Test list collection mapping over multidata input Commit: 9e3de244d7184d059e7d19cce01386e99ad85f14 https://github.com/galaxyproject/galaxy/commit/9e3de244d7184d059e7d19cce013… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix mapping list over multidata input Commit: 7cfbb032f61bbaf77be198117ba8eaa4b081c094 https://github.com/galaxyproject/galaxy/commit/7cfbb032f61bbaf77be198117ba8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/functional/tools/for_workflows/cat_collection.xml Log Message: ----------- Break test by adding "list" to collection_type This will break tests trying to map over list:pair collections, for instance test_extract_workflows_with_dataset_collections. Commit: b53d2ae3817f2c58f5e1b9f0763ee7b16cc13b81 https://github.com/galaxyproject/galaxy/commit/b53d2ae3817f2c58f5e1b9f0763e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py Log Message: ----------- Fix can_map_over for mapping over paired inputs We'd only try mapping over the first collection type description otherwise. I suppose we didn't notice because the first type is `list` and therefore much more common. Noticed this while working on https://github.com/galaxyproject/galaxy/pull/5640. Commit: f5aec1cdf18d44d4f3dc74811f421f346fc3c0f7 https://github.com/galaxyproject/galaxy/commit/f5aec1cdf18d44d4f3dc74811f42… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py Log Message: ----------- Fix inferring output structure when mapping over Previously this would have always generated `list:list` structures, even when the input is a list:pair. I'm not 100% convinced this is correct, but this seems to work. Commit: 647ba8531acdf576cfefea71bc7bb73a89ed7a0a https://github.com/galaxyproject/galaxy/commit/647ba8531acdf576cfefea71bc7b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test tool and workflow for mapping over with mapping output This doesn't quite work because of the dynamic output collection, which fails with: ``` galaxy.tools.parameters.output_collect DEBUG 2018-06-06 18:40:38,784 (3) Add dynamic collection datasets to history for output [reverse] (171.970 ms) galaxy.tools.parameters.output_collect ERROR 2018-06-06 18:40:38,839 Problem gathering output collection. Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 340, in collect_dynamic_outputs collection_builder.populate() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 88, in populate elements = self.build_elements() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 59, in build_elements new_elements[identifier] = element.build() AttributeError: 'HistoryDatasetAssociation' object has no attribute 'build' ``` This seems to happen because the inner collection is wrongly detected as nested. In general I doubt that mapping over colleciton output works with dynamically discovered output collections. Commit: 5e32d78aa7daba492ce31577481f983bd1580b68 https://github.com/galaxyproject/galaxy/commit/5e32d78aa7daba492ce31577481f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Consider mapping-over when picking collection_type for dynamically discovered collections Commit: 333d660556129b66f0bb9e3a117f9003a4bfb368 https://github.com/galaxyproject/galaxy/commit/333d660556129b66f0bb9e3a117f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Recover the correct DataCollectionToolParameter when checking if a collection is being mapped over Commit: 128a1731e42c5eb4cdf7edf939f7a5c5b3eddbc7 https://github.com/galaxyproject/galaxy/commit/128a1731e42c5eb4cdf7edf939f7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Merge pull request #6360 from guerler/legacy_modal_scrolling [18.05] Fix size handling in legacy modal view Commit: b8536c2005c69c42b20509b770f3888a5cbc80e8 https://github.com/galaxyproject/galaxy/commit/b8536c2005c69c42b20509b770f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/for_workflows/cat_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'jmchilton/collection_fixes' into release_18.05 Commit: bcf105cbb37a1c16b2109192c1271b2f4d5847d8 https://github.com/galaxyproject/galaxy/commit/bcf105cbb37a1c16b2109192c127… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/layout/modal.js M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Client build. Compare: https://github.com/galaxyproject/galaxy/compare/44b42e7e7e01...bcf105cbb37a **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] c601a9: Fix collection mapping to allow mapping over multi...
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: c601a9d4915388196dc7b00d9cc4090af2b95937 https://github.com/galaxyproject/galaxy/commit/c601a9d4915388196dc7b00d9cc4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py Log Message: ----------- Fix collection mapping to allow mapping over multi-data inputs. It is jarring to users that works for collection inputs but not multiple data inputs, especially because the IUC discourages collection inputs when multiple data inputs would work. Commit: 6b8b862e4d0d6195fb85f4c91419e115dd5564ee https://github.com/galaxyproject/galaxy/commit/6b8b862e4d0d6195fb85f4c91419… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix up subcollection_type Commit: 6b7ee55bac71859c26936a7a154dad6e090047d3 https://github.com/galaxyproject/galaxy/commit/6b7ee55bac71859c26936a7a154d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/api/test_tools.py Log Message: ----------- Test list collection mapping over multidata input Commit: 9e3de244d7184d059e7d19cce01386e99ad85f14 https://github.com/galaxyproject/galaxy/commit/9e3de244d7184d059e7d19cce013… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix mapping list over multidata input Commit: 7cfbb032f61bbaf77be198117ba8eaa4b081c094 https://github.com/galaxyproject/galaxy/commit/7cfbb032f61bbaf77be198117ba8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/functional/tools/for_workflows/cat_collection.xml Log Message: ----------- Break test by adding "list" to collection_type This will break tests trying to map over list:pair collections, for instance test_extract_workflows_with_dataset_collections. Commit: b53d2ae3817f2c58f5e1b9f0763ee7b16cc13b81 https://github.com/galaxyproject/galaxy/commit/b53d2ae3817f2c58f5e1b9f0763e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/parameters/history_query.py Log Message: ----------- Fix can_map_over for mapping over paired inputs We'd only try mapping over the first collection type description otherwise. I suppose we didn't notice because the first type is `list` and therefore much more common. Noticed this while working on https://github.com/galaxyproject/galaxy/pull/5640. Commit: f5aec1cdf18d44d4f3dc74811f421f346fc3c0f7 https://github.com/galaxyproject/galaxy/commit/f5aec1cdf18d44d4f3dc74811f42… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py Log Message: ----------- Fix inferring output structure when mapping over Previously this would have always generated `list:list` structures, even when the input is a list:pair. I'm not 100% convinced this is correct, but this seems to work. Commit: 647ba8531acdf576cfefea71bc7bb73a89ed7a0a https://github.com/galaxyproject/galaxy/commit/647ba8531acdf576cfefea71bc7b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test tool and workflow for mapping over with mapping output This doesn't quite work because of the dynamic output collection, which fails with: ``` galaxy.tools.parameters.output_collect DEBUG 2018-06-06 18:40:38,784 (3) Add dynamic collection datasets to history for output [reverse] (171.970 ms) galaxy.tools.parameters.output_collect ERROR 2018-06-06 18:40:38,839 Problem gathering output collection. Traceback (most recent call last): File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 340, in collect_dynamic_outputs collection_builder.populate() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 88, in populate elements = self.build_elements() File "/Users/mvandenb/src/galaxy/lib/galaxy/dataset_collections/builder.py", line 59, in build_elements new_elements[identifier] = element.build() AttributeError: 'HistoryDatasetAssociation' object has no attribute 'build' ``` This seems to happen because the inner collection is wrongly detected as nested. In general I doubt that mapping over colleciton output works with dynamically discovered output collections. Commit: 5e32d78aa7daba492ce31577481f983bd1580b68 https://github.com/galaxyproject/galaxy/commit/5e32d78aa7daba492ce31577481f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Consider mapping-over when picking collection_type for dynamically discovered collections Commit: 333d660556129b66f0bb9e3a117f9003a4bfb368 https://github.com/galaxyproject/galaxy/commit/333d660556129b66f0bb9e3a117f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M lib/galaxy/tools/actions/__init__.py Log Message: ----------- Recover the correct DataCollectionToolParameter when checking if a collection is being mapped over Commit: b8536c2005c69c42b20509b770f3888a5cbc80e8 https://github.com/galaxyproject/galaxy/commit/b8536c2005c69c42b20509b770f3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-content.js M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/history_query.py M lib/galaxy/tools/wrappers.py M test/api/test_tools.py M test/api/test_workflows.py A test/functional/tools/collection_type_source_map_over.xml M test/functional/tools/for_workflows/cat_collection.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge remote-tracking branch 'jmchilton/collection_fixes' into release_18.05 Commit: bcf105cbb37a1c16b2109192c1271b2f4d5847d8 https://github.com/galaxyproject/galaxy/commit/bcf105cbb37a1c16b2109192c127… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M static/scripts/bundled/libs.bundled.js M static/scripts/layout/modal.js M static/scripts/mvc/ui/ui-select-content.js Log Message: ----------- Client build. Compare: https://github.com/galaxyproject/galaxy/compare/128a1731e42c...bcf105cbb37a **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/usegalaxy-playbook] 6ca6ce: Increase RNA STAR memory factor for indexed jobs
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6ca6ce7451f37ddd0d020dd1bed403a8ccff838b https://github.com/galaxyproject/usegalaxy-playbook/commit/6ca6ce7451f37ddd… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M env/common/files/galaxy/dynamic_rules/multi_dynamic_walltime.py Log Message: ----------- Increase RNA STAR memory factor for indexed jobs **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] 69c8ce: Fix size handling in legacy modal view
by GitHub 20 Jun '18

20 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: 69c8ce7e92ff41341dff855df3149ae90ca619ed https://github.com/galaxyproject/galaxy/commit/69c8ce7e92ff41341dff855df314… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Fix size handling in legacy modal view Commit: 9f4926bd9a4f35040126cfcaa6a41c7024c3035a https://github.com/galaxyproject/galaxy/commit/9f4926bd9a4f35040126cfcaa6a4… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Limit modal body size to 67 percent of window height Commit: 128a1731e42c5eb4cdf7edf939f7a5c5b3eddbc7 https://github.com/galaxyproject/galaxy/commit/128a1731e42c5eb4cdf7edf939f7… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-20 (Wed, 20 Jun 2018) Changed paths: M client/galaxy/scripts/layout/modal.js Log Message: ----------- Merge pull request #6360 from guerler/legacy_modal_scrolling [18.05] Fix size handling in legacy modal view Compare: https://github.com/galaxyproject/galaxy/compare/817d043f1235...128a1731e42c **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

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[galaxyproject/galaxy] f6888a: Add fasta datatype to msa viewer
by GitHub 19 Jun '18

19 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy Commit: f6888a32d68d4f1be0b09257a390754a85319da3 https://github.com/galaxyproject/galaxy/commit/f6888a32d68d4f1be0b09257a390… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Add fasta datatype to msa viewer Commit: b0212ff45cf0bc6964278aac49cc42b0ebebdb65 https://github.com/galaxyproject/galaxy/commit/b0212ff45cf0bc6964278aac49cc… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Add phylip for msa viewer Commit: 817d043f123563c77e8b430f95d347bbd482d49e https://github.com/galaxyproject/galaxy/commit/817d043f123563c77e8b430f95d3… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-19 (Tue, 19 Jun 2018) Changed paths: M config/plugins/visualizations/msa/config/msa.xml Log Message: ----------- Merge pull request #6361 from guerler/fix_msa [18.05] Add fasta datatype to msa viewer Compare: https://github.com/galaxyproject/galaxy/compare/bde05ac88b66...817d043f1235 **NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/ Functionality will be removed from GitHub.com on January 31st, 2019.

1 0