Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 45ac2de349e0acd64be5e66189c74c9404e2d5da https://github.com/galaxyproject/galaxy/commit/45ac2de349e0acd64be5e66189c74... Author: John Chilton <jmchilton@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/d020522650a9bfc86c22923a01fd5... Author: John Chilton <jmchilton@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/b92074e6ff87a19133b4d97357777... Author: John Chilton <jmchilton@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/e5d5b16a446d07075378969aafa2a... Author: John Chilton <jmchilton@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/0613e038e7292d1648432926e873f... Author: John Chilton <jmchilton@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/81b5ca564ac7cdd855cb74dad8e98... Author: John Chilton <jmchilton@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/0eab8346b3dd3ee7788c9cdda0f10... Author: John Chilton <jmchilton@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/a2e31403753c407e7f6966b69b157... Author: John Chilton <jmchilton@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/9f9a4fbf497241d2de23369a3ca0f... Author: John Chilton <jmchilton@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/57652e5671c5581b3179bc5475c56... Author: John Chilton <jmchilton@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/31fc1c608cda3f049e017c0b37c29... Author: John Chilton <jmchilton@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/b8a6302aa8e062962a74d29504afe... Author: John Chilton <jmchilton@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/f7549f81813ef2b3b19d0f3c071bf... Author: John Chilton <jmchilton@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/e5758ea4e8a9cf4782e76a4228711... Author: John Chilton <jmchilton@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/3b70182877da1c357c2440141d3d6... Author: John Chilton <jmchilton@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/2f015881c4416ec7e490a786849b9... Author: guerler <aysam.guerler@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/fa27f3c63ce9d82b44077b67f939f... Author: guerler <aysam.guerler@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/c34c3a574b208be2f544b469168dc... Author: John Chilton <jmchilton@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/db59b9b70368e26a3130ead795e9c... Author: Björn Grüning <bjoern@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