- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] f59b13: Replace non-existent `tab` format with `tabular` i...
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f59b13c1cdb8e688d6738463ce54027e53d61cb7 https://github.com/galaxyproject/galaxy/commit/f59b13c1cdb8e688d6738463ce54… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml Log Message: ----------- Replace non-existent `tab` format with `tabular` in 2 tools Also: - Remove deprecated `interpreter` attribute of `<command>` - Single-quote text and data parameters inside the command - Fix wrong `name` attribute of `output` in 3 tests - Linting and cleanups Commit: b454bef75de0730b80820326eb53c2501b8baa05 https://github.com/galaxyproject/galaxy/commit/b454bef75de0730b80820326eb53… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-04 (Mon, 04 Jun 2018) Changed paths: M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml Log Message: ----------- Fix indentation Commit: 542dbe63e89689daec88ab0d075ad7f1f77bf0b0 https://github.com/galaxyproject/galaxy/commit/542dbe63e89689daec88ab0d075a… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M tools/phenotype_association/gpass.xml M tools/phenotype_association/lps.xml M tools/phenotype_association/master2gd_snp.xml M tools/phenotype_association/master2pg.xml Log Message: ----------- Merge pull request #6269 from nsoranzo/phenotype_association_tools Fixes for phenotype association tools Compare: https://github.com/galaxyproject/galaxy/compare/9b9ab6a1cf44...542dbe63e896 **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] 713bca: Allow #if $datasets #end if patern for file lists
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 713bca04f63f464ccbb47ced90d971624ed075b6 https://github.com/galaxyproject/galaxy/commit/713bca04f63f464ccbb47ced90d9… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Allow #if $datasets #end if patern for file lists Otherwise the following exception occurs: ``` Traceback (most recent call last): File "/home/wolffj/src/galaxy/lib/galaxy/jobs/runners/__init__.py", line 191, in prepare_job job_wrapper.prepare() File "/home/wolffj/src/galaxy/lib/galaxy/jobs/__init__.py", line 858, in prepare self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build() File "/home/wolffj/src/galaxy/lib/galaxy/tools/evaluation.py", line 435, in build raise e AttributeError: 'DatasetListWrapper' object has no attribute 'value' ``` This is because DatasetListWrapper inherits `__bool__` from ToolParameterValueWrapper which defines bool as ``` def __bool__(self): return bool(self.value) __nonzero__ = __bool__ ``` while DatasetListWrapper has no `value` attribute. Fixes https://github.com/galaxyproject/galaxy/issues/6314 reported by @joachimwolff (many thanks for the detailed report!). Commit: 0a29e533d3362e3a0dd7bfc202e8fff799a9e6ee https://github.com/galaxyproject/galaxy/commit/0a29e533d3362e3a0dd7bfc202e8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M test/functional/tools/multi_data_optional.xml Log Message: ----------- Use #if $datasets #end if pattern in test tool Commit: 6f213b36975b5b8f66b0b02f8920744a5e2d0064 https://github.com/galaxyproject/galaxy/commit/6f213b36975b5b8f66b0b02f8920… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/wrappers.py Log Message: ----------- Fix __bool__ for empty optional multidata parameters Commit: 550eb882100a3a9210689dbe789b67a1eb2ba5c2 https://github.com/galaxyproject/galaxy/commit/550eb882100a3a9210689dbe789b… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M test/functional/tools/multi_data_optional.xml Log Message: ----------- Add a test for not providing an optional input Commit: 9b9ab6a1cf4485920c88b252d27642f6f20c3525 https://github.com/galaxyproject/galaxy/commit/9b9ab6a1cf4485920c88b252d276… Author: Helena Rasche <hxr(a)hx42.org> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/wrappers.py M test/functional/tools/multi_data_optional.xml Log Message: ----------- Merge pull request #6317 from mvdbeek/fix_6314 Allow #if $datasets #end if pattern for file lists Compare: https://github.com/galaxyproject/galaxy/compare/c08f7c9a4cfd...9b9ab6a1cf44 **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] 6ad419: Fix undefined success_message
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6ad41928093c033568eeb3e530f32a813accb24e https://github.com/galaxyproject/galaxy/commit/6ad41928093c033568eeb3e530f3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js Log Message: ----------- Fix undefined success_message Commit: c08f7c9a4cfdf4da4771b7f891892ea1332666dc https://github.com/galaxyproject/galaxy/commit/c08f7c9a4cfdf4da4771b7f89189… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/form/form-wrapper.js Log Message: ----------- Merge pull request #6316 from mvdbeek/success_message_fix Fix undefined success_message Compare: https://github.com/galaxyproject/galaxy/compare/254a6bc8d793...c08f7c9a4cfd **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] b46ab9: Fix typo (UnitializedTree -> UninitializedTree)
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b46ab962adcaef54b75b8e9bf3e5647b59b128cc https://github.com/galaxyproject/galaxy/commit/b46ab962adcaef54b75b8e9bf3e5… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Fix typo (UnitializedTree -> UninitializedTree) Commit: 254a6bc8d7939a385783795aba6f1fb4a7c4677d https://github.com/galaxyproject/galaxy/commit/254a6bc8d7939a385783795aba6f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/upload.py M lib/galaxy/tools/parameters/output_collect.py Log Message: ----------- Merge pull request #6315 from mvdbeek/fix_uninitialized_typo Fix typo (UnitializedTree -> UninitializedTree) Compare: https://github.com/galaxyproject/galaxy/compare/1b50504678dc...254a6bc8d793 **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] 6c2f19: Rules - test case and bug fixes for adding cols fo...
by GitHub 12 Jun '18

12 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c2f1957a9c49943182b8b971097f9a8ef511bab https://github.com/galaxyproject/galaxy/commit/6c2f1957a9c49943182b8b971097… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/util/rules_dsl.py M test/base/data/rules_dsl_spec.yml Log Message: ----------- Rules - test case and bug fixes for adding cols for regex groups. Commit: 898e73eca1eccfb9fb707cdb5af75ee72c3d7565 https://github.com/galaxyproject/galaxy/commit/898e73eca1eccfb9fb707cdb5af7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/managers/collections.py Log Message: ----------- Rules - bug fix for apply_rules tool on nested collections. Commit: ec723829bf788b3100bfb56f72c22dd4981e3fdf https://github.com/galaxyproject/galaxy/commit/ec723829bf788b3100bfb56f72c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-04 (Fri, 04 May 2018) Changed paths: M lib/galaxy/tools/apply_rules.xml Log Message: ----------- Rules - fix poor name for Apply Rules output collection. Commit: 050c9e99c6c981518f160d99aeaa2f395a84e4b5 https://github.com/galaxyproject/galaxy/commit/050c9e99c6c981518f160d99aeaa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-05-05 (Sat, 05 May 2018) Changed paths: A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Rules - test case for apply rules tutorial. Demonstrates using the Apply Rules collection operation tool against existing collections to: - Use grouping to build nested lists from flat ones. - Invert nested collections. - Filter collections. - Filter while also grouping to build nested collections. Based on count data used in the DESeq2 tutorial (http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq…) originally from the Bioconductor Pasilla package (http://bioconductor.org/packages/release/data/experiment/html/pasilla.html) Citation: Huber W, Reyes A (2018). pasilla: Data package with per-exon and per-gene read counts of RNA-seq samples of Pasilla knock-down by Brooks et al., Genome Research 2011.. R package version 1.8.0. Commit: 1b50504678dc5c84fa292236ac58697591611aa4 https://github.com/galaxyproject/galaxy/commit/1b50504678dc5c84fa292236ac58… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2018-06-12 (Tue, 12 Jun 2018) Changed paths: M lib/galaxy/tools/apply_rules.xml A test-data/rules/treated1fb.txt A test-data/rules/treated2fb.txt A test-data/rules/treated3fb.txt A test-data/rules/untreated1fb.txt A test-data/rules/untreated2fb.txt A test-data/rules/untreated3fb.txt A test-data/rules/untreated4fb.txt M test/galaxy_selenium/navigates_galaxy.py M test/selenium_tests/test_tool_form.py Log Message: ----------- Merge pull request #6066 from jmchilton/apply_rules_tutorials Rules - test case for apply rules tutorial. Compare: https://github.com/galaxyproject/galaxy/compare/178486b840b6...1b50504678dc **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] 940ed5: Break test by adding "list" to collection_type
by GitHub 11 Jun '18

11 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 940ed5f5dd1f34456d81513db8bbf0a66476e683 https://github.com/galaxyproject/galaxy/commit/940ed5f5dd1f34456d81513db8bb… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-08 (Fri, 08 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: cb97f89d129cf7f0b7cf7146c0c15309b3dcb0c7 https://github.com/galaxyproject/galaxy/commit/cb97f89d129cf7f0b7cf7146c0c1… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-08 (Fri, 08 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: 9b19d5c267900409b5aace9f2c554b2da13ce8e7 https://github.com/galaxyproject/galaxy/commit/9b19d5c267900409b5aace9f2c55… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 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: fd16302d65193f13eb04456b610044343ca54adb https://github.com/galaxyproject/galaxy/commit/fd16302d65193f13eb04456b6100… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 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: 258ccb89bd5190e703f9d1705ec888b65ce77724 https://github.com/galaxyproject/galaxy/commit/258ccb89bd5190e703f9d1705ec8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 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: fc06a7a168d5d36fabb3f6f420a4ef0b12363f2c https://github.com/galaxyproject/galaxy/commit/fc06a7a168d5d36fabb3f6f420a4… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2018-06-11 (Mon, 11 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: 178486b840b64c2bfb1b4cffefd44c945a8ccb3e https://github.com/galaxyproject/galaxy/commit/178486b840b64c2bfb1b4cffefd4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M lib/galaxy/dataset_collections/structure.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/history_query.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 pull request #6278 from mvdbeek/fix_paired_mapping_over Various fixes for mapping over collections Compare: https://github.com/galaxyproject/galaxy/compare/cd2feb7dcb81...178486b840b6 **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] 1b5edc: Updated RNAStar on test and main to version 2.6.0b
by GitHub 11 Jun '18

11 Jun '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1b5edc4e15bcbd5db7e8774e0a5504413c365f5a https://github.com/galaxyproject/usegalaxy-playbook/commit/1b5edc4e15bcbd5d… Author: Dave B <dave(a)bx.psu.edu> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/main/files/galaxy/var/shed_tool_conf.xml M env/main/files/galaxy/var/shed_tool_data_table_conf.xml M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Updated RNAStar on test and main to version 2.6.0b **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] 39dc8c: Revise job success message
by GitHub 11 Jun '18

11 Jun '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 39dc8cfac9a9f090e433ef94e01025329ba421e7 https://github.com/galaxyproject/galaxy/commit/39dc8cfac9a9f090e433ef94e010… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Revise job success message Commit: 8e55b22542ff4a7118294efeab296ccc5849db84 https://github.com/galaxyproject/galaxy/commit/8e55b22542ff4a7118294efeab29… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Sort history items by history id in success message Commit: 086bf43eeb3362a775a62420f430156b19b1df19 https://github.com/galaxyproject/galaxy/commit/086bf43eeb3362a775a62420f430… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-06-06 (Wed, 06 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Hide inputs for tools without inputs Commit: 106dda140f322734c6c4917a54b137c418840a99 https://github.com/galaxyproject/galaxy/commit/106dda140f322734c6c4917a54b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Missing semicolon. Commit: 80e1590869527627ede01954d0a4271ca05304bf https://github.com/galaxyproject/galaxy/commit/80e1590869527627ede01954d0a4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Client format Commit: cd2feb7dcb81424e753ef371879c3f4b397555b6 https://github.com/galaxyproject/galaxy/commit/cd2feb7dcb81424e753ef371879c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form.js Log Message: ----------- Merge branch 'job_success_message' into dev Compare: https://github.com/galaxyproject/galaxy/compare/99c1da2f6273...cd2feb7dcb81 **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 11 Jun '18

11 Jun '18

Branch: refs/heads/dev 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: 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: 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: 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: 99c1da2f62739654d72a598908ea07b7d2e699a7 https://github.com/galaxyproject/galaxy/commit/99c1da2f62739654d72a598908ea… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-06-11 (Mon, 11 Jun 2018) Changed paths: M client/galaxy/scripts/components/HistoryView.vue M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/tours.js M client/galaxy/style/scss/base.scss M lib/galaxy/jobs/handler.py M lib/galaxy/jobs/runners/slurm.py M scripts/grt/grt.yml.sample M static/style/blue/base.css Log Message: ----------- Merge branch 'release_18.05' into dev Compare: https://github.com/galaxyproject/galaxy/compare/44275a2b722f...99c1da2f6273 **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] 5a0f98: Strip a spurious Slurm warning from job stderr
by GitHub 11 Jun '18

11 Jun '18

Branch: refs/heads/release_18.05 Home: https://github.com/galaxyproject/galaxy 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: 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 Compare: https://github.com/galaxyproject/galaxy/compare/dba21dc8a426...e7b7bee82e60 **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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