December 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 914adf: Sychronize tool shed, planemo, and toolbox code fo...
by GitHub 22 Dec '15

22 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 914adfcc0cd5e8b060df059da9a4f8e9b1293fde https://github.com/galaxyproject/galaxy/commit/914adfcc0cd5e8b060df059da9a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/toolbox/base.py M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Sychronize tool shed, planemo, and toolbox code for filtering out non-tool XML files. A single abstraction will allow toolbox and planemo to deal with other kinds of tools in the future, and the stronger preconditions should eliminate some busy error logging when monitoring a tool directory. Commit: 20b47f3ca208ded3682f68591f5801b85547efc1 https://github.com/galaxyproject/galaxy/commit/20b47f3ca208ded3682f68591f58… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Update looks_like_a_tool to respect enable_beta_tool_formats. Default is off obviously, so for instance the tool shed will never think unsupported beta tools are real tools. Commit: a8ed6146e88642b17273e316c571c5a5a9f4df45 https://github.com/galaxyproject/galaxy/commit/a8ed6146e88642b17273e316c571… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/util/odict.py Log Message: ----------- Tweak YAML tools to use ordered dictionaries. Order of inputs and outputs in Galaxy is important, so preserve this order if using dictionary-style (both available) for inputs and/or outputs. Commit: b7b8f097d5a7617b2997f254b4e0229adfaae623 https://github.com/galaxyproject/galaxy/commit/b7b8f097d5a7617b2997f254b4e0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-18 (Fri, 18 Dec 2015) Changed paths: M lib/galaxy/tools/parser/yaml.py Log Message: ----------- Enhance YAML/dictionary tool rep. to allow output collections. Commit: f874d559b7db28c3fa7b4df6844f077da419911a https://github.com/galaxyproject/galaxy/commit/f874d559b7db28c3fa7b4df6844f… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/odict.py M lib/tool_shed/metadata/metadata_generator.py Log Message: ----------- Merge pull request #1368 from jmchilton/looks_like_a_tool Unify and Abstract Code for Checking if File Looks Like a Tool Compare: https://github.com/galaxyproject/galaxy/compare/ae2b94824a32...f874d559b7db

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[galaxyproject/usegalaxy-playbook] b77be7: Split out the installer config so it can use a loc...
by GitHub 22 Dec '15

22 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b77be75830614dcc86bd95c8ef544176f9909c78 https://github.com/galaxyproject/usegalaxy-playbook/commit/b77be75830614dcc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-22 (Tue, 22 Dec 2015) Changed paths: M galaxy.yml M galaxy_configs.yml M production/group_vars/galaxyservers.yml M stage/group_vars/galaxyservers.yml M templates/supervisor/galaxy_installer.conf.j2 Log Message: ----------- Split out the installer config so it can use a local temp for performance reasons.

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[galaxyproject/usegalaxy-playbook] 988f3e: install cummerbund to Main
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 988f3ed096f701f0c6cb19823b8b879ac124e684 https://github.com/galaxyproject/usegalaxy-playbook/commit/988f3ed096f701f0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- install cummerbund to Main

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[galaxyproject/usegalaxy-playbook] ca7987: update Main
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: ca79873a365c88c0975f43d772bb0448c9e8bcb2 https://github.com/galaxyproject/usegalaxy-playbook/commit/ca79873a365c88c0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- update Main

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[galaxyproject/usegalaxy-playbook] 947b92: rename Main section properly
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 947b929da5e262abd6b72ea5946ea0bb5e52004b https://github.com/galaxyproject/usegalaxy-playbook/commit/947b929da5e262ab… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- rename Main section properly

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[galaxyproject/usegalaxy-playbook] c18f04: install hisat2 and sailfish on Main
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c18f04b1c81e84273be5dcc505becaabba04949c https://github.com/galaxyproject/usegalaxy-playbook/commit/c18f04b1c81e8427… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml Log Message: ----------- install hisat2 and sailfish on Main

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[galaxyproject/usegalaxy-playbook] b7b3ff: install stringtie on Main mutable confs
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b7b3ff65ba942a2a696863a4943e33ef20aff32e https://github.com/galaxyproject/usegalaxy-playbook/commit/b7b3ff65ba942a2a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- install stringtie on Main mutable confs

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[galaxyproject/usegalaxy-playbook] e7ce1f: update Main mutable confs
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e7ce1fa72d714e3035e22076ae3ebfbe2b7c71fd https://github.com/galaxyproject/usegalaxy-playbook/commit/e7ce1fa72d714e30… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- update Main mutable confs

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[galaxyproject/usegalaxy-playbook] 72e6c4: rename Main tool section
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 72e6c4fa10e5c82b461d41693fa7871cbca1624a https://github.com/galaxyproject/usegalaxy-playbook/commit/72e6c4fa10e5c82b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- rename Main tool section

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[galaxyproject/usegalaxy-playbook] 1c3697: update Main mutable confs
by GitHub 21 Dec '15

21 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 1c3697c2cb0581617d02a2e55eac525d5922a3f3 https://github.com/galaxyproject/usegalaxy-playbook/commit/1c3697c2cb058161… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-21 (Mon, 21 Dec 2015) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- update Main mutable confs

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