February 2016 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] 137e8b: update MTS
by GitHub 29 Feb '16

29 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 137e8b34960321b9b9608897813dccf1bf724c6d https://github.com/galaxyproject/usegalaxy-playbook/commit/137e8b34960321b9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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[galaxyproject/galaxy] 5bc55f: Add js for mako based masthead
by GitHub 29 Feb '16

29 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 5bc55f9fa2fd6af9142df644bf82e830b56f9ce4 https://github.com/galaxyproject/galaxy/commit/5bc55f9fa2fd6af9142df644bf82… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Add js for mako based masthead Commit: 281f5b734610963b437b72837e7b71cebbb3c5bd https://github.com/galaxyproject/galaxy/commit/281f5b734610963b437b72837e7b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/ui/popup-menu.js M client/galaxy/scripts/mvc/workflow/workflow-terminals.js M client/galaxy/style/less/base.less M client/galaxy/style/less/fontawesome/core.less M client/galaxy/style/less/ui/icon-btn.less M doc/source/releases/16.01.rst M doc/source/releases/16.01_announce.rst M lib/galaxy/config.py M lib/galaxy/exceptions/__init__.py M lib/galaxy/exceptions/error_codes.json M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/version.py M lib/galaxy/web/base/interactive_environments.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/tool_shed/capsule/capsule_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/util/commit_util.py M lib/tool_shed/util/encoding_util.py M lib/tool_shed/util/repository_content_util.py M lib/tool_shed/util/shed_util_common.py M static/maps/mvc/ui/popup-menu.js.map M static/maps/mvc/workflow/workflow-terminals.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/popup-menu.js M static/scripts/mvc/workflow/workflow-terminals.js M static/style/blue/base.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/history/display.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test/functional/tools/output_format.xml M test/qunit/tests/workflow_editor_tests.js M test/tool_shed/base/twilltestcase.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge branch 'release_16.01' of https://github.com/galaxyproject/galaxy into release_16.01 Commit: fa8beb225004d27da24065f8f633c7917b5be942 https://github.com/galaxyproject/galaxy/commit/fa8beb225004d27da24065f8f633… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M templates/webapps/tool_shed/base_panels.mako Log Message: ----------- Merge pull request #1823 from martenson/port-masthead-fix [16.01] Port masthead fix Compare: https://github.com/galaxyproject/galaxy/compare/47c93180708e...fa8beb225004

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[galaxyproject/galaxy] aeb008: Implement dataset empty input validator.
by GitHub 29 Feb '16

29 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aeb008ca43621bb87a58675764ab04eaa24b5608 https://github.com/galaxyproject/galaxy/commit/aeb008ca43621bb87a58675764ab… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/validation.py M test/api/test_tools.py A test/functional/tools/empty_output.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_empty_dataset.xml Log Message: ----------- Implement dataset empty input validator. Commit: e43c2ef5dea09864bf59339c738f0b32b85d8ef5 https://github.com/galaxyproject/galaxy/commit/e43c2ef5dea09864bf59339c738f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/tools/parameters/validation.py M test/api/test_tools.py A test/functional/tools/empty_output.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/validation_empty_dataset.xml Log Message: ----------- Merge pull request #1808 from jmchilton/empty_dataset Implement dataset empty input validator. Compare: https://github.com/galaxyproject/galaxy/compare/052187b80cd8...e43c2ef5dea0

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[galaxyproject/galaxy] c78451: Initial swap from svgfig to svgwrite, more or less...
by GitHub 29 Feb '16

29 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c78451f1bd0487109591cf81740c1d5a10f3d2ae https://github.com/galaxyproject/galaxy/commit/c78451f1bd0487109591cf81740c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py Log Message: ----------- Initial swap from svgfig to svgwrite, more or less drop-in replacement of the same rendering approach and look/feel. Commit: 0db0655b10ad47631b636300635e87530b057d94 https://github.com/galaxyproject/galaxy/commit/0db0655b10ad47631b636300635e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Both uses need to .tostring() the canvas, not just the first one. Commit: 872bcbc4ead7694583c5d398dc799f862aff8a0a https://github.com/galaxyproject/galaxy/commit/872bcbc4ead7694583c5d398dc79… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Arrow aesthetics, simplification; some magic number replacement. Commit: f7c41623ae9abaacaf30044954f48e8ab858d1ed https://github.com/galaxyproject/galaxy/commit/f7c41623ae9abaacaf30044954f4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt Log Message: ----------- Add svgwrite wheel. Commit: 6f72338b449c9f92ca8a58e42f898716b0edcc74 https://github.com/galaxyproject/galaxy/commit/6f72338b449c9f92ca8a58e42f89… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt Log Message: ----------- Remove svgfig and add svgwrite hash from pinned reqs. Commit: 4dce3e35d75fdf94938b70a56d28ace806c907b8 https://github.com/galaxyproject/galaxy/commit/4dce3e35d75fdf94938b70a56d28… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/tool_shed/util/workflow_util.py M test/unit/workflows/test_render.py Log Message: ----------- Toolshed/test swaps from standalone_xml to tostring Commit: c4350b4ab9e3e367f0101109b6db404d32ab0eb9 https://github.com/galaxyproject/galaxy/commit/c4350b4ab9e3e367f0101109b6db… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/workflow/render.py Log Message: ----------- Font styling/sizing to match original behavior. Commit: 052187b80cd8f11d72bea4aa18f15ee94aad56cb https://github.com/galaxyproject/galaxy/commit/052187b80cd8f11d72bea4aa18f1… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/dependencies/pinned-hashed-requirements.txt M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/render.py M lib/tool_shed/util/workflow_util.py M test/unit/workflows/test_render.py Log Message: ----------- Merge pull request #1747 from dannon/svg_lib_swap Swapping from svgfig to svgwrite Compare: https://github.com/galaxyproject/galaxy/compare/1019f7b40fcb...052187b80cd8

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[galaxyproject/galaxy] 0dac0c: Refactor workflow loading.
by GitHub 29 Feb '16

29 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0dac0c207757cf160901df387214dcfc56016469 https://github.com/galaxyproject/galaxy/commit/0dac0c207757cf160901df387214… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-15 (Mon, 15 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Refactor workflow loading. Remove even more duplication between updating and creating workflows. A few new test cases to verify errors under certain conditions. Commit: 92d978dd9d9b15bab7b3852787c2ce094880f97d https://github.com/galaxyproject/galaxy/commit/92d978dd9d9b15bab7b3852787c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-16 (Tue, 16 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Eliminate from_editor param to simplify workflow manager... ... slightly. Commit: 1019f7b40fcb916c96dc62dafeee8bffeb44f33a https://github.com/galaxyproject/galaxy/commit/1019f7b40fcb916c96dc62dafeee… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-02-29 (Mon, 29 Feb 2016) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/galaxy/workflow/modules.py M test/api/test_workflows.py Log Message: ----------- Merge pull request #1735 from jmchilton/more_wf_loading_dup Refactor workflow loading. Compare: https://github.com/galaxyproject/galaxy/compare/14f58261bd77...1019f7b40fcb

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[galaxyproject/galaxy] 56076d: Disable command isolation for Pulsar...
by GitHub 28 Feb '16

28 Feb '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 56076db848459cb1da39b04dc635538ff013d3a9 https://github.com/galaxyproject/galaxy/commit/56076db848459cb1da39b04dc635… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py Log Message: ----------- Disable command isolation for Pulsar... ... it builds its own job script - no need to have Galaxy do this isolation on the Galaxy end. The more Pulsar can handle the better. Commit: cb19630bd4e04b21653a2cb9848e888805dfabcc https://github.com/galaxyproject/galaxy/commit/cb19630bd4e04b21653a2cb9848e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Fix unit tests for 56076db848459cb1da39b04dc635538ff013d3a9 Commit: 47c93180708eb138c1fa0393cd18b24d27249359 https://github.com/galaxyproject/galaxy/commit/47c93180708eb138c1fa0393cd18… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-28 (Sun, 28 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/pulsar.py M test/unit/jobs/test_job_wrapper.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #1812 from jmchilton/pulsar_16.01_fixes [16.01] Disable command isolation for Pulsar... Compare: https://github.com/galaxyproject/galaxy/compare/dad1784a0876...47c93180708e

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[galaxyproject/galaxy] 9b4b20: Reduce the use of mutable types in method definiti...
by GitHub 28 Feb '16

28 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b4b20cb887b290c671c4f2941dfd25c6439b73e https://github.com/galaxyproject/galaxy/commit/9b4b20cb887b290c671c4f2941df… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Reduce the use of mutable types in method definitions. Commit: 14f58261bd771fe54108efccb081199171d3bd0f https://github.com/galaxyproject/galaxy/commit/14f58261bd771fe54108efccb081… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-28 (Sun, 28 Feb 2016) Changed paths: M test/tool_shed/base/twilltestcase.py Log Message: ----------- Merge pull request #1813 from davebx/mutable_types Reduce the use of mutable types in toolshed test framework's method definitions. Compare: https://github.com/galaxyproject/galaxy/compare/db59b9b70368...14f58261bd77

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[galaxyproject/galaxy] 45ac2d: Revert "Switch default job shell back to /bin/sh f...
by GitHub 27 Feb '16

27 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45ac2de349e0acd64be5e66189c74c9404e2d5da https://github.com/galaxyproject/galaxy/commit/45ac2de349e0acd64be5e66189c7… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Revert "Switch default job shell back to /bin/sh for 16.01." This reverts commit 602dc7f6649d96086b85ed0d309eef7c4ed73a13. 16.04 will use bash as the default. Commit: d020522650a9bfc86c22923a01fd5d7c07c65326 https://github.com/galaxyproject/galaxy/commit/d020522650a9bfc86c22923a01fd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml M test/unit/jobs/test_command_factory.py Log Message: ----------- Introduce strict shell command option. Newer tool formats (CWL and YAML just enable this by default), but XML tools can add a strict="true" to the command block to force "set -e" handling on the shell part of tool execution. Run the framework tests verifying the new and older default behavior using the following commands: ``` ./run_tests.sh -framework -id strict_shell_default_off ./run_tests.sh -framework -id strict_shell ``` Commit: b92074e6ff87a19133b4d973577779c4ee6286d7 https://github.com/galaxyproject/galaxy/commit/b92074e6ff87a19133b4d9735777… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_evaluation.py Log Message: ----------- Implement profile="XX.XX" on tools, better defaults for newer tools. - set -e in tool command scripts. - Disable implicit extra file collection. All dynamic extra file collection requires a <discover_datasets tag. - Disable format="input" - require explicit metadata targets (metadata_source, format_source). - Disable interpreter= - hacky and doesn't work as expected in too many circumstances. Use $__tool_directory__. - Disable $param_file - grepping the command for the string is impercise. If useful we can add flag to match the flag used to produce inputs as a JSON file. - Disable default version of 1.0.0, the IUC has made it clear they prefer all tools have an explicit version. Fixes #1609. Commit: e5d5b16a446d07075378969aafa2a0ff4aa97bbc https://github.com/galaxyproject/galaxy/commit/e5d5b16a446d07075378969aafa2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/util/job_script/__init__.py Log Message: ----------- Simplify pbs runner. Just reuse parent class methods, these are just different ways of executing the same actions essentially. Commit: 0613e038e7292d1648432926e873fba26ba5b23f https://github.com/galaxyproject/galaxy/commit/0613e038e7292d1648432926e873… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/runners/cli.py Log Message: ----------- Remove legacy job support from CLI runner. Commit: 81b5ca564ac7cdd855cb74dad8e98abc83a8efdc https://github.com/galaxyproject/galaxy/commit/81b5ca564ac7cdd855cb74dad8e9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py Log Message: ----------- Make more job options configurable at the destination level. Makes a host of job-related parameters configurable at the destination level instead of the of only at the app level. This solves major problems like allowing the local job runner and the drmma run as real-user runner to operate within in the same environment and provides little conveniences like allowing configuration of cleanup job at the destination level. Commit: 0eab8346b3dd3ee7788c9cdda0f10f8aea4b2726 https://github.com/galaxyproject/galaxy/commit/0eab8346b3dd3ee7788c9cdda0f1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/config.py M lib/galaxy/objectstore/__init__.py M test/unit/test_objectstore.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Rename config.job_working_directory to config.jobs_directory. Commit: a2e31403753c407e7f6966b69b157e32f5f3ef8a https://github.com/galaxyproject/galaxy/commit/a2e31403753c407e7f6966b69b15… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/parameters/output_collect.py M test/unit/jobs/test_command_factory.py Log Message: ----------- Give tool executions a clean working directory. Rather then massively renaming job_directory and job_working_directory, I introduce the concept of the tool execution working directory (tool_working_directory) that is the job working directory + "/working" and that will not be populated with job files. Some legacy cruft in there for the upgrade, things like galaxy.json and dynamic outputs may be in the job working directory or the tool execution working directory. Commit: 9f9a4fbf497241d2de23369a3ca0fdd0ff01fada https://github.com/galaxyproject/galaxy/commit/9f9a4fbf497241d2de23369a3ca0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/command_factory.py Log Message: ----------- Greater resiliency against bad job script commands... ... when building tool execution commands using the command_factory's CommandBuilder. Commit: 57652e5671c5581b3179bc5475c56a4d1283bd62 https://github.com/galaxyproject/galaxy/commit/57652e5671c5581b3179bc5475c5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/parser/cwl.py Log Message: ----------- Updated CWL module for downstream changes and draft 3 support. Commit: 31fc1c608cda3f049e017c0b37c293743336dd7e https://github.com/galaxyproject/galaxy/commit/31fc1c608cda3f049e017c0b37c2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Fix YAML jobs for setting tool.description as None. XML tools would set this as '' and there are places it is assumed to be a string. Commit: b8a6302aa8e062962a74d29504afe01dd646373e https://github.com/galaxyproject/galaxy/commit/b8a6302aa8e062962a74d29504af… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_parsing.py Log Message: ----------- Migrate tool sanitize and refresh options to parser framework. Trying to get everything in there in general and need to disable sanitize for CWL tools downstream using this override point. Commit: f7549f81813ef2b3b19d0f3c071bf147dd5e09bb https://github.com/galaxyproject/galaxy/commit/f7549f81813ef2b3b19d0f3c071b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Cleanup for destination config changes. Commit: e5758ea4e8a9cf4782e76a4228711b69b8dc1650 https://github.com/galaxyproject/galaxy/commit/e5758ea4e8a9cf4782e76a422871… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- Rebase into config destinations. Commit: 3b70182877da1c357c2440141d3d602c453eafb2 https://github.com/galaxyproject/galaxy/commit/3b70182877da1c357c2440141d3d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-22 (Mon, 22 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Improve tool loading problem messages. Include tool paths, IDs, etc... where appropriate. Commit: 2f015881c4416ec7e490a786849b991c9d958f6f https://github.com/galaxyproject/galaxy/commit/2f015881c4416ec7e490a786849b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_evaluation.py Log Message: ----------- Revise legacy handling Commit: fa27f3c63ce9d82b44077b67f939f35fc7d50a98 https://github.com/galaxyproject/galaxy/commit/fa27f3c63ce9d82b44077b67f939… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M test/unit/tools/test_evaluation.py Log Message: ----------- Add spaces Commit: c34c3a574b208be2f544b469168dce75d88b7f99 https://github.com/galaxyproject/galaxy/commit/c34c3a574b208be2f544b469168d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/unit/tools/test_evaluation.py Log Message: ----------- Merge pull request #44 from guerler/revise_tool_profile_000 Revise legacy handling Commit: db59b9b70368e26a3130ead795e9c3166b3cb59b https://github.com/galaxyproject/galaxy/commit/db59b9b70368e26a3130ead795e9… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-28 (Sun, 28 Feb 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/cli.py M lib/galaxy/jobs/runners/condor.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/jobs/runners/pbs.py M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/representation.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parser/cwl.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/interface.py M lib/galaxy/tools/parser/output_collection_def.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml M test/unit/jobs/test_command_factory.py M test/unit/test_objectstore.py M test/unit/tools/test_evaluation.py M test/unit/tools/test_parsing.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #1688 from jmchilton/16.04_jobs Overhaul of Tools and Jobs for 16.04 Compare: https://github.com/galaxyproject/galaxy/compare/da50cf114923...db59b9b70368

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[galaxyproject/usegalaxy-playbook] 49261b: Update Test
by GitHub 26 Feb '16

26 Feb '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 49261bdc3f1a092467fa6ddc620843c75dad98c9 https://github.com/galaxyproject/usegalaxy-playbook/commit/49261bdc3f1a0924… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

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[galaxyproject/galaxy] 6d9ac0: Ensure tool.changeset_revision is set...
by GitHub 26 Feb '16

26 Feb '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d9ac081c1fa164382de7a351b90790899636b54 https://github.com/galaxyproject/galaxy/commit/6d9ac081c1fa164382de7a351b90… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Ensure tool.changeset_revision is set... ... in some cases tool.tool_shed will be non-null but changeset_revision will be absent. This is my development instance so it is easy to imagine my database doesn't match my tool panel config. Commit: da50cf114923b241f1e4c6fc1d90f920207170cf https://github.com/galaxyproject/galaxy/commit/da50cf114923b241f1e4c6fc1d90… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1806 from jmchilton/changeset_problems_fix Ensure tool.changeset_revision is set... Compare: https://github.com/galaxyproject/galaxy/compare/453345c6210f...da50cf114923

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