Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d4f9955a66c94604634d436a4262cfef395b3e5 https://github.com/galaxyproject/galaxy/commit/8d4f9955a66c94604634d436a4262... Author: John Chilton <jmchilton@gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_command_factory.py M test/unit/tools_support.py Log Message: ----------- Limit adjusting Galaxy's Python environment to legacy tools. Don't expose Galaxy's environment to tools unless there is evidence we need to. This should restrict future bugs by limitting what tools are exposed to Galaxy's internals and will fix bugs related to Conda dependencies masking Galaxy - such as #2994. Should fix #2994. Rebased with language and tool best practice fixes thanks to @mvdbeek. Commit: 7bac8bbc786ba9697cf1e0a0e8597c8d06aa1721 https://github.com/galaxyproject/galaxy/commit/7bac8bbc786ba9697cf1e0a0e8597... Author: Marius van den Beek <m.vandenbeek@gmail.com> Date: 2017-01-03 (Tue, 03 Jan 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/command_factory.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh M lib/galaxy/jobs/runners/util/job_script/__init__.py M lib/galaxy/tools/__init__.py A test/functional/tools/python_environment_problem.py A test/functional/tools/python_environment_problem.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_command_factory.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #3364 from jmchilton/clean_python Limit adjusting Galaxy's Python environment to legacy tools. Compare: https://github.com/galaxyproject/galaxy/compare/85333d4be474...7bac8bbc786b