- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 3e18d5: Increase max walltime for Jetstream jobs for Du No...
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3e18d57835e51c48d17366fed93027a536d41e05 https://github.com/galaxyproject/infrastructure-playbook/commit/3e18d57835e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M jetstream_common/templates/slurm/slurm.conf.j2 Log Message: ----------- Increase max walltime for Jetstream jobs for Du Novo: Align Families (how did this work before)?

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[galaxyproject/usegalaxy-playbook] 4d11e2: Main integrated tool panel
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4d11e2dadd455daba11c24eae5a039d7e488717a https://github.com/galaxyproject/usegalaxy-playbook/commit/4d11e2dadd455dab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M env/main/files/galaxy/var/integrated_tool_panel.xml Log Message: ----------- Main integrated tool panel Commit: 2d2db24e8d099282666f5acda432305aeb887a04 https://github.com/galaxyproject/usegalaxy-playbook/commit/2d2db24e8d099282… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M env/common/stack.yml M env/main/_inc_config_post_tasks.yml M env/main/group_vars/galaxyservers/vars.yml A env/test/files/nginx/tacc-protected/index.html M env/test/group_vars/webservers/vars.yml M env/test/group_vars/webservers/vault.yml A env/test/templates/nginx/nginx_galaxy.pam.j2 M env/test/templates/nginx/tacc_protected.j2 Log Message: ----------- Fix Main impersonation and other protected stuff Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/f0726c237e5c...…

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[galaxyproject/galaxy] bf6896: Fix get_tool returning list when it shouldn't.
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bf68966accd18af2da1e4fa518d01119f5a696f2 https://github.com/galaxyproject/galaxy/commit/bf68966accd18af2da1e4fa518d0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix get_tool returning list when it shouldn't. Commit: 4a35bd3532ce3a9e0af84c3a86ee33585e9e0ba3 https://github.com/galaxyproject/galaxy/commit/4a35bd3532ce3a9e0af84c3a86ee… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #4390 from jmchilton/toollist Fix get_tool returning list when it shouldn't. Compare: https://github.com/galaxyproject/galaxy/compare/d53a5424967e...4a35bd3532ce

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[galaxyproject/galaxy] ecad39: Refactor ToolOutputCollectionStructure to allow it...
by GitHub 08 Aug '17

08 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ecad3996f1f4715db5ff326f9f6ae5067cd2e0fc https://github.com/galaxyproject/galaxy/commit/ecad3996f1f4715db5ff326f9f6a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Refactor ToolOutputCollectionStructure to allow it be more easily consumed. Make complex arguments optional. Commit: e8112210429d710a9eb9702f541cfaed6e219454 https://github.com/galaxyproject/galaxy/commit/e8112210429d710a9eb9702f541c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Improve cohesion of interaction between ToolOutputCollectionStructure and ToolOutputCollection. Shield more of ToolOutputCollectionStructure internals from ToolOutputCollection. Commit: d53a5424967e46d683f7baafe06cb53703e86adf https://github.com/galaxyproject/galaxy/commit/d53a5424967e46d683f7baafe06c… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-08-08 (Tue, 08 Aug 2017) Changed paths: M lib/galaxy/tools/parser/output_objects.py Log Message: ----------- Merge pull request #4389 from jmchilton/output_collect_refactor Refactor ToolOutputCollectionStructure... Compare: https://github.com/galaxyproject/galaxy/compare/d2394aa172e2...d53a5424967e

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[galaxyproject/galaxy] 15cc6e: Async update 20170615
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 15cc6e461a9d921c9762a54a112f74abc9353309 https://github.com/galaxyproject/galaxy/commit/15cc6e461a9d921c9762a54a112f… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Async update 20170615 The asynchronous procedure expects that only one output is defined in the tool XML schema. This improvement permits to define also collections. This feature is useful in conjunction with tools like [galaxy-json-collect-data-source](https://github.com/fabio-cumbo/galaxy- json-collect-data-source) (please see the README of the tool for more information). It does not affect the behaviour of the asynchronous data sources previously developed. Commit: b4fdc27f533a0a204f9eedfcd265a15ef0fb469e https://github.com/galaxyproject/galaxy/commit/b4fdc27f533a0a204f9eedfcd265… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Blank line contains whitespace: fixed Commit: d5409500aebe1c5798ae632977be64b8f71a85a8 https://github.com/galaxyproject/galaxy/commit/d5409500aebe1c5798ae632977be… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- minor update 20170711 if GALAXY_TYPE is provided, we do not need to loop over tool.outputs.values() Commit: e516ba738ecbb13f29d072fd0ad707f8470369de https://github.com/galaxyproject/galaxy/commit/e516ba738ecbb13f29d072fd0ad7… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- except Exception: fixed Commit: 835e4fb0ae09c12a8db80ca6f3d339275f3881f0 https://github.com/galaxyproject/galaxy/commit/835e4fb0ae09c12a8db80ca6f3d3… Author: Fabio Cumbo <fabio.cumbo(a)gmail.com> Date: 2017-07-12 (Wed, 12 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- outputs count: fixed Commit: d2394aa172e2030c301f7b50863fb3d96664a2db https://github.com/galaxyproject/galaxy/commit/d2394aa172e2030c301f7b50863f… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/async.py Log Message: ----------- Merge pull request #4198 from fabio-cumbo/data-source-async Async update: support to collections Compare: https://github.com/galaxyproject/galaxy/compare/6e37bc05c1d5...d2394aa172e2

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[galaxyproject/galaxy] b19640: Stop loading tools that require a newer galaxy
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b19640b81a83af2759666717ae658940103588fe https://github.com/galaxyproject/galaxy/commit/b19640b81a83af2759666717ae65… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Stop loading tools that require a newer galaxy We look at a tools profile attribute, and if it is too new we will not load the tool. This is a first step towards https://github.com/galaxyproject/galaxy/issues/2086 Commit: 6e37bc05c1d5ce247c0f371799a69e9f064168b4 https://github.com/galaxyproject/galaxy/commit/6e37bc05c1d5ce247c0f371799a6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/toolbox/base.py M test/unit/tools/test_toolbox.py M test/unit/tools_support.py Log Message: ----------- Merge pull request #4382 from mvdbeek/enforce_tool_profiles Stop loading tools that require a newer galaxy Compare: https://github.com/galaxyproject/galaxy/compare/5be7768047f4...6e37bc05c1d5

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[galaxyproject/galaxy] 6943c7: Allow import of history archives via siple file up...
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6943c74556858f89703567c4558e885291d95c57 https://github.com/galaxyproject/galaxy/commit/6943c74556858f89703567c4558e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Allow import of history archives via siple file upload Commit: 5be7768047f471d49a85525bd0aa9bd814b081aa https://github.com/galaxyproject/galaxy/commit/5be7768047f471d49a85525bd0aa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/history.py Log Message: ----------- Merge pull request #4326 from mvdbeek/history_import_from_file Allow import of history archives via simple file upload Compare: https://github.com/galaxyproject/galaxy/compare/31f68edbbaf9...5be7768047f4

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[galaxyproject/galaxy] 1f2fa3: Reuse Shell objects after initialization
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1f2fa31963b56c79072ae36a09ddf6a31a5e9683 https://github.com/galaxyproject/galaxy/commit/1f2fa31963b56c79072ae36a09dd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/__init__.py A test/unit/test_remote_shell.py Log Message: ----------- Reuse Shell objects after initialization Commit: 330fe392096f68d34c964ae2cb62d454f609fc3c https://github.com/galaxyproject/galaxy/commit/330fe392096f68d34c964ae2cb62… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M lib/galaxy/jobs/runners/util/cli/shell/local.py Log Message: ----------- Sleep 100 ms before polling process This should be long enough for most shell commands and speed up the average time to check a job's status. Commit: 5a37bc263feeb7be2411d555ebb3e03359c488aa https://github.com/galaxyproject/galaxy/commit/5a37bc263feeb7be2411d555ebb3… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/shell/rsh.py M test/unit/test_remote_shell.py Log Message: ----------- Add a new Paramiko-based shell runner and tests This allows a single ssh connection to be reused. The unit test also tests the current SecureShell class. The unit tests require [mock-ssh-server](https://github.com/carletes/mock-ssh-server). These tests are being skipped if this library is not importable. Commit: 69365e49eaeea173f3ecaad17d1f4bcefa65c316 https://github.com/galaxyproject/galaxy/commit/69365e49eaeea173f3ecaad17d1f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M tox.ini Log Message: ----------- Install mock-ssh-server or unit testing Commit: 31f68edbbaf9fdccd3582bde5b20b43728251755 https://github.com/galaxyproject/galaxy/commit/31f68edbbaf9fdccd3582bde5b20… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/util/cli/__init__.py M lib/galaxy/jobs/runners/util/cli/shell/local.py M lib/galaxy/jobs/runners/util/cli/shell/rsh.py A test/unit/test_remote_shell.py M tox.ini Log Message: ----------- Merge pull request #4358 from mvdbeek/paramiko_based_shell_runner Paramiko based shell runner Compare: https://github.com/galaxyproject/galaxy/compare/3e1b46fe42ad...31f68edbbaf9

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[galaxyproject/galaxy] 2e31a5: Add test tool for API tests
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e31a5b6d18c62411cc419fb5dfd3008bd7a14df https://github.com/galaxyproject/galaxy/commit/2e31a5b6d18c62411cc419fb5dfd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: A test/functional/tools/identifier_source.xml Log Message: ----------- Add test tool for API tests Commit: b4c72eaccf07c9ee0d7e93de21311f0c6d9cc6c4 https://github.com/galaxyproject/galaxy/commit/b4c72eaccf07c9ee0d7e93de2131… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M test/functional/tools/identifier_source.xml Log Message: ----------- Fix the command section (thx @nsoranzo) Commit: 3e1b46fe42ad57aa8a1f8c2d0752cfd4bed47ad4 https://github.com/galaxyproject/galaxy/commit/3e1b46fe42ad57aa8a1f8c2d0752… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: A test/functional/tools/identifier_source.xml Log Message: ----------- Merge pull request #4380 from mvdbeek/tie_down_collection_matcher Add test tool for API tests Compare: https://github.com/galaxyproject/galaxy/compare/e92a15a18523...3e1b46fe42ad

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[galaxyproject/galaxy] 9d6a0e: Implement default_identifier_source for outputs
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9d6a0e82f6f9634981ea96c37f0f48e38e9c5b12 https://github.com/galaxyproject/galaxy/commit/9d6a0e82f6f9634981ea96c37f0f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/xsd/galaxy.xsd Log Message: ----------- Implement default_identifier_source for outputs This allows tool authors to specify an input from which the element identifier can be inherited. This applies only to non-collection output when mapping a collection over an input, since collections have a structured_like attribute. Commit: 35c0a4770336ca82fda7dd3034fd029e3bd474b8 https://github.com/galaxyproject/galaxy/commit/35c0a4770336ca82fda7dd3034fd… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M test/api/test_tools.py M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add test API test for default_identifier_source Commit: 46fba6ec1c728125efa1339e7334202487a09e18 https://github.com/galaxyproject/galaxy/commit/46fba6ec1c728125efa1339e7334… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/dataset_collections/matching.py Log Message: ----------- Sort input keys by default, so the first matching input key will the source of the element identifiers Commit: ea15f398e79771b6dd6ba5fdf0c8d96e10d39734 https://github.com/galaxyproject/galaxy/commit/ea15f398e79771b6dd6ba5fdf0c8… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/tools/execute.py Log Message: ----------- Fix failing API tests for explicit collection outputs Commit: e92a15a18523e14c050d987b3c14be412fcaaddc https://github.com/galaxyproject/galaxy/commit/e92a15a18523e14c050d987b3c14… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/dataset_collections/matching.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/parser/yaml.py M lib/galaxy/tools/xsd/galaxy.xsd M test/api/test_tools.py M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #4368 from mvdbeek/tie_down_collection_matcher Implement default_identifier_source for outputs and sort input keys by default Compare: https://github.com/galaxyproject/galaxy/compare/68c7b0982bb1...e92a15a18523

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