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

[galaxyproject/galaxy] e3ced2: Fix migration 0137's downgrade -- previously faile...
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: e3ced2c669485f76eae7fcfb3b32aa048730964d https://github.com/galaxyproject/galaxy/commit/e3ced2c669485f76eae7fcfb3b32… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py Log Message: ----------- Fix migration 0137's downgrade -- previously failed to select the correct column to drop Commit: c8407786f25c98c87f441f15222f72eeea4edc72 https://github.com/galaxyproject/galaxy/commit/c8407786f25c98c87f441f15222f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-26 (Mon, 26 Feb 2018) Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py Log Message: ----------- Merge pull request #5605 from dannon/migrate_fix [18.01] Fix migration 0137's downgrade Compare: https://github.com/galaxyproject/galaxy/compare/fc52fe5c6270...c8407786f25c

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[galaxyproject/galaxy] 291527: Update to latest galaxy-lib.
by GitHub 26 Feb '18

26 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 291527226755f7cf3210bb2f2d550ee1248184cd https://github.com/galaxyproject/galaxy/commit/291527226755f7cf3210bb2f2d55… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-25 (Sun, 25 Feb 2018) 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/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/command.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Update to latest galaxy-lib. Includes: - Fixes for multi-requirement container building via mulled via https://github.com/galaxyproject/galaxy-lib/pull/84. - Fixes for Conda search problems https://github.com/galaxyproject/galaxy-lib/pull/83. - Updates to CWL library support https://github.com/galaxyproject/galaxy-lib/pull/78. - Make bz2file dependency optional (xref https://github.com/galaxyproject/galaxy-lib/pull/79) - Python 3 fixes for path stuff - runtime fixes caught because galaxy-lib runs tests using Python 3 https://github.com/galaxyproject/galaxy-lib/pull/85/commits/c056e39451ca8b4… and https://github.com/galaxyproject/galaxy-lib/pull/85/commits/c7cc9caba389770…) - Python 3 fix for linter (https://github.com/galaxyproject/galaxy-lib/pull/88/commits/17d167662cda2ae…) Commit: a6c8317d1d5d1eaa633c8a06d2ba9cd02c472716 https://github.com/galaxyproject/galaxy/commit/a6c8317d1d5d1eaa633c8a06d2ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-25 (Sun, 25 Feb 2018) Changed paths: M lib/galaxy/tools/deps/commands.py Log Message: ----------- Bring in Nicola's Python 3 fixes. https://github.com/galaxyproject/galaxy-lib/commit/fcfb1aed1a08760857d5154a… https://github.com/galaxyproject/galaxy-lib/commit/704b2400a5cbfdb49d60508c… Commit: 2af4091e42b621720602734db5e408f28fe64fe4 https://github.com/galaxyproject/galaxy/commit/2af4091e42b621720602734db5e4… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2018-02-26 (Mon, 26 Feb 2018) 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/cwl/schema.py A lib/galaxy/tools/cwl/util.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/requirements.py M lib/galaxy/tools/linters/command.py M lib/galaxy/util/__init__.py M lib/galaxy/util/checkers.py M lib/galaxy/util/compression_utils.py M lib/galaxy/util/path/__init__.py Log Message: ----------- Merge pull request #5602 from jmchilton/galaxy-lib-update-20180223 Update against galaxy-lib Compare: https://github.com/galaxyproject/galaxy/compare/91a0c0342166...2af4091e42b6

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[galaxyproject/galaxy] 8c80ce: move the cache from toolbox level to tool level
by GitHub 25 Feb '18

25 Feb '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8c80ce73b0c581426fa71baa4005ce6a11930fd1 https://github.com/galaxyproject/galaxy/commit/8c80ce73b0c581426fa71baa4005… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- move the cache from toolbox level to tool level the cache remains toolbox-specific so it is stored within the toolbox object includes refactor thanks to eagle eyes Commit: 91a0c0342166d0a615a265b326b219df88c99aa0 https://github.com/galaxyproject/galaxy/commit/91a0c0342166d0a615a265b326b2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-02-25 (Sun, 25 Feb 2018) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #5600 from martenson/move-cache-deeper move the cache from toolbox level to the tool level Compare: https://github.com/galaxyproject/galaxy/compare/f354b9d3f589...91a0c0342166

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[galaxyproject/usegalaxy-playbook] 026989: Disable additional GenomeSpace tools
by GitHub 23 Feb '18

23 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 026989f9e41990d5d2374134e07a5925fbd7b071 https://github.com/galaxyproject/usegalaxy-playbook/commit/026989f9e41990d5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/main/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/config/tool_conf.xml Log Message: ----------- Disable additional GenomeSpace tools

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[galaxyproject/usegalaxy-playbook] 81b6ba: Main mutable configs
by GitHub 23 Feb '18

23 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 81b6badbfdf7383ce76faa54029676f0202f992c https://github.com/galaxyproject/usegalaxy-playbook/commit/81b6badbfdf7383c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 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 Log Message: ----------- Main mutable configs Commit: dbf235bc8e64bbbf43f472dc255af3628ca685de https://github.com/galaxyproject/usegalaxy-playbook/commit/dbf235bc8e64bbbf… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/main/files/galaxy/config/tool_conf.xml M env/test/files/galaxy/config/tool_conf.xml Log Message: ----------- Temporarily disable GenomeSpace Importer due to problems Commit: b1294a3daa9b184807ee530b22e7b4aac0f3ebeb https://github.com/galaxyproject/usegalaxy-playbook/commit/b1294a3daa9b1848… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Temporarily disable GenomeSpace Importer due to problems with the tool Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/85499c50c73c...…

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[galaxyproject/usegalaxy-playbook] acb5d7: Run MAFFT as a multi job. Fixes #65
by GitHub 23 Feb '18

23 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: acb5d7af1c92c53a47f5dbef672819fddf2f4f5f https://github.com/galaxyproject/usegalaxy-playbook/commit/acb5d7af1c92c53a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/main/templates/galaxy/config/job_conf.xml.j2 M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run MAFFT as a multi job. Fixes #65 Commit: 85499c50c73cbee32cba99b89734d4d922d517d2 https://github.com/galaxyproject/usegalaxy-playbook/commit/85499c50c73cbee3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-23 (Fri, 23 Feb 2018) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml M env/test/files/galaxy/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/574921ff0d98...…

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[galaxyproject/galaxy] 880603: Replace distutils.version with packaging.version
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 8806030f53c2b9d0002505bf5193be88d7cff8f9 https://github.com/galaxyproject/galaxy/commit/8806030f53c2b9d0002505bf5193… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Replace distutils.version with packaging.version distutils under Python3 has this bug: https://bugs.python.org/issue14894 which causes this traceback: ``` Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 125, in __init__ self._configure_toolbox() File "lib/galaxy/config.py", line 930, in _configure_toolbox self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self) File "lib/galaxy/tools/__init__.py", line 232, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__ self._load_tool_panel() File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel self.__add_tool_to_tool_panel(section_val, section, section=True) File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel related_tool = self._lineage_in_panel(panel_dict, tool=tool) File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel lineage_tool_versions = reversed(tool_lineage.get_versions()) File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids return ["%s/%s" % (tool_id, version) for version in self.tool_versions] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions return sorted(self._tool_versions, key=LooseVersion) File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__ c = self._cmp(other) File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ``` when a tool version contains a letter in the "wrong" place (e.g. in the first position). Fix https://github.com/galaxyproject/galaxy/issues/5408 . Commit: fc52fe5c62700b4f8527e4edead0fba4e7cfe33f https://github.com/galaxyproject/galaxy/commit/fc52fe5c62700b4f8527e4edead0… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #5588 from jmchilton/backport_packaging [18.01] Replace distutils.version with packaging.version Compare: https://github.com/galaxyproject/galaxy/compare/ce3b40cfc10e...fc52fe5c6270

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[galaxyproject/usegalaxy-playbook] 574921: Main: Increase Pulsar stream size
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 574921ff0d989aeb9e31e6229b59d0dadf72df29 https://github.com/galaxyproject/usegalaxy-playbook/commit/574921ff0d989aeb… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/main/host_vars/br005.bridges.psc.edu.yml M env/main/host_vars/jetstream-iu0.galaxyproject.org.yml M env/main/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/main/host_vars/login5.stampede.tacc.utexas.edu.yml Log Message: ----------- Main: Increase Pulsar stream size

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[galaxyproject/usegalaxy-playbook] 560c91: Main mutable config
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 560c9178467903dbe14f7643cceaf41c922f239d https://github.com/galaxyproject/usegalaxy-playbook/commit/560c9178467903db… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Main mutable config Commit: abe7ecf5bc6c490883844dedcc43442aeefbe3fc https://github.com/galaxyproject/usegalaxy-playbook/commit/abe7ecf5bc6c4908… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M roles/usegalaxy_cvmfs/tasks/update.yml Log Message: ----------- Eliminate docker restart as it's no longer needed. Commit: 749403d897d4ed0cfa0ece17829208835edcb650 https://github.com/galaxyproject/usegalaxy-playbook/commit/749403d897d4ed0c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/main/group_vars/ftpservers/vars.yml M env/test/group_vars/ftpservers/vars.yml Log Message: ----------- Increase FTP upload limit to 75 GB Commit: dd1a8a790db92e7773c6853e7bbda3fff9611f7b https://github.com/galaxyproject/usegalaxy-playbook/commit/dd1a8a790db92e77… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/test/host_vars/br005.bridges.psc.edu.yml M env/test/host_vars/jetstream-iu0.galaxyproject.org.yml M env/test/host_vars/jetstream-tacc0.galaxyproject.org.yml M env/test/host_vars/login5.stampede.tacc.utexas.edu.yml Log Message: ----------- Increase Test Pulsar stream limits to 8 MB Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/8f88cb0342a4...…

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[galaxyproject/usegalaxy-playbook] 8f88cb: Main: Disable BioMart, enable @nuwang's GenomeSpac...
by GitHub 22 Feb '18

22 Feb '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8f88cb0342a4c5ceace6511ada0732657ee5b82d https://github.com/galaxyproject/usegalaxy-playbook/commit/8f88cb0342a4c5ce… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-02-22 (Thu, 22 Feb 2018) Changed paths: M env/main/files/galaxy/config/tool_conf.xml Log Message: ----------- Main: Disable BioMart, enable @nuwang's GenomeSpace updates, add new collection operations

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