- galaxy-commits - lists.galaxyproject.org

[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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[galaxyproject/galaxy] 9803dc: More updates to GRT
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9803dc600cb62235d9a1abad15e5b7b4877be2aa https://github.com/galaxyproject/galaxy/commit/9803dc600cb62235d9a1abad15e5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- More updates to GRT Commit: 5abbf1102ed93b5d78bb126a571cef8e07a95b4e https://github.com/galaxyproject/galaxy/commit/5abbf1102ed93b5d78bb126a571c… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.py Log Message: ----------- at loop time Commit: b0428352e07d444b58d428da2928608005647491 https://github.com/galaxyproject/galaxy/commit/b0428352e07d444b58d428da2928… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: A scripts/grt-submit.py M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- Split out the submission portion Commit: c14d37fbd6717a97ca700c5f4bb507444df570b9 https://github.com/galaxyproject/galaxy/commit/c14d37fbd6717a97ca700c5f4bb5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.py Log Message: ----------- timings Commit: 163127b4b2c513a810ece57d8deb1851123a9351 https://github.com/galaxyproject/galaxy/commit/163127b4b2c513a810ece57d8deb… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.py Log Message: ----------- Also dump toolbox Commit: 2cd2c3967a74dacbdd3d920935fe141e65675043 https://github.com/galaxyproject/galaxy/commit/2cd2c3967a74dacbdd3d920935fe… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.yml.sample Log Message: ----------- document GRT a bit more Commit: 11ac796f2df407ff2f547324842333591a543daa https://github.com/galaxyproject/galaxy/commit/11ac796f2df407ff2f5473248423… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M scripts/grt.py Log Message: ----------- Include hash for transport Commit: d453231226543face2eee1c7d652029450b056fd https://github.com/galaxyproject/galaxy/commit/d453231226543face2eee1c7d652… Author: E Rasche <hxr(a)hx42.org> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- Various optimisations Commit: a0292a46c7f966d4f1c70a5cc19320f8255d64b1 https://github.com/galaxyproject/galaxy/commit/a0292a46c7f966d4f1c70a5cc193… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt-submit.py M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- Revert submission of instance metadata Commit: 93eac6dfcf8d2517381c0cff3b10429ae97aacad https://github.com/galaxyproject/galaxy/commit/93eac6dfcf8d2517381c0cff3b10… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- remove redundant code Commit: 50156d8e7be4cb7693cd3e92ccd5df682b4799a6 https://github.com/galaxyproject/galaxy/commit/50156d8e7be4cb7693cd3e92ccd5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt-submit.py Log Message: ----------- import from grt Commit: df33d4f7080bd75a5d2e25ec20469ebc2ac54574 https://github.com/galaxyproject/galaxy/commit/df33d4f7080bd75a5d2e25ec2046… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- Super optimised GRT Commit: 07faeaa5ce2645be8e2ce9bfc61f1b8d8658505a https://github.com/galaxyproject/galaxy/commit/07faeaa5ce2645be8e2ce9bfc61f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- Batched sql queries, sanitization Commit: 94a8a9a841c4352c8dccfd42844f4fab2c97db7c https://github.com/galaxyproject/galaxy/commit/94a8a9a841c4352c8dccfd42844f… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- default to sharing toolbox Commit: cf4dc28c5fa762c93dcc2fd51d42a7bb684f7ecb https://github.com/galaxyproject/galaxy/commit/cf4dc28c5fa762c93dcc2fd51d42… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- Disable sanitization by default Commit: cefa47c6986429ba37949f49b849e624d226a62e https://github.com/galaxyproject/galaxy/commit/cefa47c6986429ba37949f49b849… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.yml.sample Log Message: ----------- remove keys from testing Commit: 6caded21251539c721907c281c8cd83b4797391e https://github.com/galaxyproject/galaxy/commit/6caded21251539c721907c281c8c… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- unused function Commit: 5e6d1cba409f082a3f2e7748d6eb1fa8010c4470 https://github.com/galaxyproject/galaxy/commit/5e6d1cba409f082a3f2e7748d6eb… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- Some simplification which should significantly speed up parsing Commit: 08aeea3e92158a45a3e88b5da5e8f3b31821e6ba https://github.com/galaxyproject/galaxy/commit/08aeea3e92158a45a3e88b5da5e8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py M scripts/grt.yml.sample Log Message: ----------- add headers Commit: 058c4a74b83897ba36ec548b6be8162976a549c7 https://github.com/galaxyproject/galaxy/commit/058c4a74b83897ba36ec548b6be8… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- remove text metrics Commit: 16f17efe497e39bcd5fc1f493b7e5bb810a437b2 https://github.com/galaxyproject/galaxy/commit/16f17efe497e39bcd5fc1f493b7e… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- remove remenants of __any__ Commit: 70f4bc957e9a29b85f41e35cf8530122c8284356 https://github.com/galaxyproject/galaxy/commit/70f4bc957e9a29b85f41e35cf853… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst M scripts/grt.py Log Message: ----------- update documentation and fix blacklisting bug Commit: 5ed50dba1c4478ab58b9c96e1077652675fe9b2f https://github.com/galaxyproject/galaxy/commit/5ed50dba1c4478ab58b9c96e1077… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- Allow sending subsets Commit: 7deff206226ce90b68e2e306146a1ea59c745073 https://github.com/galaxyproject/galaxy/commit/7deff206226ce90b68e2e306146a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- move up to fix print statement Commit: b381a90fcb2b4e169a133f3ff0667b4bf93375df https://github.com/galaxyproject/galaxy/commit/b381a90fcb2b4e169a133f3ff066… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt-submit.py M scripts/grt.py Log Message: ----------- flake8 Commit: d3b271761f4d2f998bea3a290e2b35389f968fe9 https://github.com/galaxyproject/galaxy/commit/d3b271761f4d2f998bea3a290e2b… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M scripts/grt.py Log Message: ----------- remove a blank line Commit: e8b367bde3d429c991d223c3d8df76399d6cff81 https://github.com/galaxyproject/galaxy/commit/e8b367bde3d429c991d223c3d8df… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: R scripts/grt-submit.py R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/grt-submit.py A scripts/grt/grt.py A scripts/grt/grt.yml.sample Log Message: ----------- move to subdir Commit: 0ed3571f0d6285d5415eeffc0a8a8f97724aab77 https://github.com/galaxyproject/galaxy/commit/0ed3571f0d6285d5415eeffc0a8a… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M scripts/grt/grt-submit.py M scripts/grt/grt.py Log Message: ----------- Fix various logging statements Commit: 7e94cf20b0bd05e73c50976cb1f5196e776ebb1e https://github.com/galaxyproject/galaxy/commit/7e94cf20b0bd05e73c50976cb1f5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M scripts/grt/grt.py Log Message: ----------- fix todo Commit: 1043ee5fd4e8eb559795e16c63f735dbbe9924a6 https://github.com/galaxyproject/galaxy/commit/1043ee5fd4e8eb559795e16c63f7… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst Log Message: ----------- update docs to reflect new locations Commit: ddcddecb4a3f049bc35fa7a6832339dc9f66bad9 https://github.com/galaxyproject/galaxy/commit/ddcddecb4a3f049bc35fa7a68323… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst A scripts/grt/export.py R scripts/grt/grt-submit.py R scripts/grt/grt.py A scripts/grt/upload.py Log Message: ----------- rename scripts Commit: 5b83c6c330f4bb8ccbe77031cd3d6db513a882f6 https://github.com/galaxyproject/galaxy/commit/5b83c6c330f4bb8ccbe77031cd3d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M scripts/grt/export.py Log Message: ----------- Merge branch 'grt-update-2' of github.com:erasche/galaxy into grt-update-2 Commit: a6fcb95a15134e9ef42cd39663ebe70dfed37fd1 https://github.com/galaxyproject/galaxy/commit/a6fcb95a15134e9ef42cd39663eb… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M scripts/grt/grt.yml.sample Log Message: ----------- default false with expl Commit: 89887689b479e34e3d049dd689a5f8c8e3f47fc2 https://github.com/galaxyproject/galaxy/commit/89887689b479e34e3d049dd689a5… Author: E Rasche <hxr(a)hx42.org> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst Log Message: ----------- correct some spelling errors Commit: 68c7b0982bb19c509cfdc87c58ac3578edf038db https://github.com/galaxyproject/galaxy/commit/68c7b0982bb19c509cfdc87c58ac… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M doc/source/admin/special_topics/grt.rst R scripts/grt.py R scripts/grt.yml.sample A scripts/grt/export.py A scripts/grt/grt.yml.sample A scripts/grt/upload.py Log Message: ----------- Merge pull request #4376 from erasche/grt-update-2 Galactic Radio Telescope Update Compare: https://github.com/galaxyproject/galaxy/compare/3f270e91afc3...68c7b0982bb1

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[galaxyproject/galaxy] 4b5247: Fix TypeError when uploading large files from ftp ...
by GitHub 07 Aug '17

07 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4b52476b24fd6cb196eac32295e6ae1a30228b2f https://github.com/galaxyproject/galaxy/commit/4b52476b24fd6cb196eac32295e6… Author: Jian-Long Huang <huang(a)jianlong.org> Date: 2017-07-14 (Fri, 14 Jul 2017) Changed paths: M lib/galaxy/objectstore/s3_multipart_upload.py Log Message: ----------- Fix TypeError when uploading large files from ftp to s3 Commit: 3f270e91afc3792233248c1f7cb9f6735b95b7f4 https://github.com/galaxyproject/galaxy/commit/3f270e91afc3792233248c1f7cb9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-07 (Mon, 07 Aug 2017) Changed paths: M lib/galaxy/objectstore/s3_multipart_upload.py Log Message: ----------- Merge pull request #4315 from jlhg/fix-s3mu-map-wrap Fix TypeError when uploading large files from ftp to s3 Compare: https://github.com/galaxyproject/galaxy/compare/4effd7d77ae7...3f270e91afc3

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[galaxyproject/galaxy] b17091: CSRF protection for login, logout, and user regist...
by GitHub 05 Aug '17

05 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b17091a3ec51a4836370f32b71ea72abfe4a966f https://github.com/galaxyproject/galaxy/commit/b17091a3ec51a4836370f32b71ea… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- CSRF protection for login, logout, and user registeration. The approach is to use per-session CSRF tokens - this avoids many complications related to per-form tokens. We generate a sequence of hashes based on session IDs that doesn't follow the same pattern as normal database API IDs by supplying a "kind" parameter to encode_id (we use the same pattern for securing the job files API for Pulsar). Commit: 4effd7d77ae75d577c5d04b34174464a43d075b8 https://github.com/galaxyproject/galaxy/commit/4effd7d77ae75d577c5d04b34174… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-05 (Sat, 05 Aug 2017) Changed paths: M client/galaxy/scripts/galaxy.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/user/user-preferences.js M lib/galaxy/web/base/controller.py M lib/galaxy/web/framework/webapp.py M lib/galaxy/webapps/galaxy/controllers/user.py M static/maps/galaxy.js.map M static/maps/layout/menu.js.map M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/galaxy.js M static/scripts/layout/menu.js M static/scripts/mvc/user/user-preferences.js M templates/galaxy_client_app.mako M templates/user/login.mako M templates/user/register.mako M test/shed_functional/base/twilltestcase.py Log Message: ----------- Merge pull request #4365 from jmchilton/csrf CSRF protection for login, logout, and user registration. Compare: https://github.com/galaxyproject/galaxy/compare/575696dcc2cc...4effd7d77ae7

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[galaxyproject/galaxy] 8d5a31: Register tool lineage when loading tool via quick_...
by GitHub 04 Aug '17

04 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d5a315671b6fd1c475abc88f454a7c3bfb434f4 https://github.com/galaxyproject/galaxy/commit/8d5a315671b6fd1c475abc88f454… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Register tool lineage when loading tool via quick_load() Commit: 51951a8850888d0d5538ef5f84327bb78ccbfba6 https://github.com/galaxyproject/galaxy/commit/51951a8850888d0d5538ef5f8432… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M lib/galaxy/jobs/rule_helper.py M lib/galaxy/model/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Always use tool version to get tools from toolbox This fixes a bug when getting parameters for jobs that were executed with old tool versions. Commit: faee2b65c29ee405d475d54a630d54c7b29a4159 https://github.com/galaxyproject/galaxy/commit/faee2b65c29ee405d475d54a630d… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Use self.job instead of self.parent_job in Task Noticed by @nsoranzo. Commit: 7474474cc0ec8f98a0e23bfd7bf2906326938153 https://github.com/galaxyproject/galaxy/commit/7474474cc0ec8f98a0e23bfd7bf2… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Move tool lineage registration to toolbox.__add_tool() Commit: ccad70c22c082b3801dec567600f054581e8044b https://github.com/galaxyproject/galaxy/commit/ccad70c22c082b3801dec567600f… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Add warnings if a tool lineage could not be retrieved Commit: 575696dcc2cc775e72b58f5cda0612a79b62b87b https://github.com/galaxyproject/galaxy/commit/575696dcc2cc775e72b58f5cda06… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-04 (Fri, 04 Aug 2017) Changed paths: M lib/galaxy/jobs/rule_helper.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M templates/webapps/galaxy/history/display_structured.mako M templates/webapps/galaxy/workflow/build_from_current_history.mako Log Message: ----------- Merge pull request #4375 from mvdbeek/tool_version_and_lineage_fixes Tool version and lineage fixes Compare: https://github.com/galaxyproject/galaxy/compare/dbd057f9d720...575696dcc2cc

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[galaxyproject/galaxy] 32bd35: Fix URL for workflow editor 'Run' button
by GitHub 04 Aug '17

04 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 32bd350fe9c06b9f506c21c9ba4eab97408c404d https://github.com/galaxyproject/galaxy/commit/32bd350fe9c06b9f506c21c9ba4e… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Fix URL for workflow editor 'Run' button On the current dev this would point to api/workflows//download?style=run and result in `Error occurred while loading the resource.` Commit: dbd057f9d72036bff98d3217312e4de3148b3285 https://github.com/galaxyproject/galaxy/commit/dbd057f9d72036bff98d3217312e… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-view.js M static/maps/mvc/workflow/workflow-view.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js Log Message: ----------- Merge pull request #4371 from mvdbeek/fix_run_from_workflow_editor Fix URL for workflow editor 'Run' button Compare: https://github.com/galaxyproject/galaxy/compare/fe3fdc82d239...dbd057f9d720

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[galaxyproject/galaxy] 910e6f: Allow removal of dataset tags in workflows
by GitHub 03 Aug '17

03 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 910e6fa035684fbdfc2b38e4675308e47e801083 https://github.com/galaxyproject/galaxy/commit/910e6fa035684fbdfc2b38e46753… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Allow removal of dataset tags in workflows This adds a RemoveTagDatasetAction PJA, which removes user-specified tags if they exist. Fixes https://github.com/galaxyproject/galaxy/issues/4362 Commit: fe3fdc82d23978c4161d8f020c256576f663e10a https://github.com/galaxyproject/galaxy/commit/fe3fdc82d23978c4161d8f020c25… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-forms.js M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/tags.py M static/maps/mvc/workflow/workflow-forms.js.map M static/scripts/mvc/workflow/workflow-forms.js Log Message: ----------- Merge pull request #4369 from mvdbeek/tag_removal Allow removal of dataset tags in workflows Compare: https://github.com/galaxyproject/galaxy/compare/6b2a2582002d...fe3fdc82d239

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[galaxyproject/galaxy] 97c16d: Add ImzML composite defintion
by GitHub 03 Aug '17

03 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 97c16db8245570196b556854570b0c120abcb8b0 https://github.com/galaxyproject/galaxy/commit/97c16db8245570196b556854570b… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Add ImzML composite defintion Commit: e2f69a9c5bc7d11274190e223493d6d12d33afb3 https://github.com/galaxyproject/galaxy/commit/e2f69a9c5bc7d11274190e223493… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- add imzml to the datatypes conf file Commit: 1d609ca2caa158422adcdee0bbc65e73ce0527d2 https://github.com/galaxyproject/galaxy/commit/1d609ca2caa158422adcdee0bbc6… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- add edam format Commit: e768e77392471a60425984ae518fb4f34a0552ee https://github.com/galaxyproject/galaxy/commit/e768e77392471a60425984ae518f… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/datatypes/proteomics.py Log Message: ----------- fix pep8 Commit: 6b2a2582002d38665b2f3def1245675d638e6c75 https://github.com/galaxyproject/galaxy/commit/6b2a2582002d38665b2f3def1245… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-08-03 (Thu, 03 Aug 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/proteomics.py Log Message: ----------- Merge pull request #4370 from bgruening/mzml Add imzML datatype Compare: https://github.com/galaxyproject/galaxy/compare/ade8844d11aa...6b2a2582002d

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[galaxyproject/galaxy] e88233: Preview feature for Bam datatype
by GitHub 02 Aug '17

02 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e88233af84d50822bc6328114e112165605e32fa https://github.com/galaxyproject/galaxy/commit/e88233af84d50822bc6328114e11… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Preview feature for Bam datatype Commit: 2005a9d685209789c95e5eb48d2a6c77d9703201 https://github.com/galaxyproject/galaxy/commit/2005a9d685209789c95e5eb48d2a… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Preview feature for Bam datatype. Final Changes Commit: bb67be81cd1c2043ecd1b1eb54942cbb5b52c828 https://github.com/galaxyproject/galaxy/commit/bb67be81cd1c2043ecd1b1eb5494… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-05 (Wed, 05 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Updated based on the changes requested Commit: 72c196f793aeb30ec00cf368e419bcdaecdbd514 https://github.com/galaxyproject/galaxy/commit/72c196f793aeb30ec00cf368e419… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Accessing Bam file via seek() and tell() Commit: c66298d62717c88cf4341ad1601176420b16f280 https://github.com/galaxyproject/galaxy/commit/c66298d62717c88cf4341ad16011… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- travis test correction Commit: 8c8aa8820fcc592c31693399660b87b04809b9da https://github.com/galaxyproject/galaxy/commit/8c8aa8820fcc592c31693399660b… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Preview feature for Bam datatype Commit: 3ddf819c83f881eee4b7ab19281926e1e64a58d3 https://github.com/galaxyproject/galaxy/commit/3ddf819c83f881eee4b7ab192819… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Preview feature for Bam datatype. Final Changes Commit: 9a8c8b8a61b1ec09509cc9b2b7738eae5238e036 https://github.com/galaxyproject/galaxy/commit/9a8c8b8a61b1ec09509cc9b2b773… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Updated based on the changes requested Commit: 731d1db4b23e2a75335f716a9c6f6d1b30938101 https://github.com/galaxyproject/galaxy/commit/731d1db4b23e2a75335f716a9c6f… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Accessing Bam file via seek() and tell() Commit: dac72950db3b64291c5c202b9db15fac3525de86 https://github.com/galaxyproject/galaxy/commit/dac72950db3b64291c5c202b9db1… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- travis test correction Commit: 635df817663ffc82fe26645512f880c16c251dd4 https://github.com/galaxyproject/galaxy/commit/635df817663ffc82fe26645512f8… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Log Message: ----------- resolving sniff.py conflict Commit: 253d0c2d4f435a9778a636ff3a162d0fe0717854 https://github.com/galaxyproject/galaxy/commit/253d0c2d4f435a9778a636ff3a16… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-06 (Thu, 06 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- reordering import statements Commit: 3ddd05d56985360c31bd62ea78027fbfc34bb796 https://github.com/galaxyproject/galaxy/commit/3ddd05d56985360c31bd62ea7802… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Removing the SAM datatype for class Bam and resetting changes with sniff.py Commit: c476090bdef84b7781458ff7445451d35e0af46b https://github.com/galaxyproject/galaxy/commit/c476090bdef84b7781458ff74454… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- setting default value for column_names, column_types and column Metadata Commit: 8b3e492bad9257bd0f4c9ba3e78f1a88cc64bfe6 https://github.com/galaxyproject/galaxy/commit/8b3e492bad9257bd0f4c9ba3e78f… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Fix for travis test Commit: 0cfdfbf275fda9072b521fa501ad1aaafdc87c8e https://github.com/galaxyproject/galaxy/commit/0cfdfbf275fda9072b521fa501ad… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-07 (Fri, 07 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- replaced last_read with offset variable Commit: 90a0ab0398860cccf84a78dd293f62b44bb0bf71 https://github.com/galaxyproject/galaxy/commit/90a0ab0398860cccf84a78dd293f… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Replace '\t' to ' ' in BAM headers Commit: b370a9cbaea3781d21c3d618cfa5521bdc5bea73 https://github.com/galaxyproject/galaxy/commit/b370a9cbaea3781d21c3d618cfa5… Author: ashvark <ashvark(a)gmail.com> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- travis test fix Commit: ade8844d11aa90a1ccda20545d6283b5635befb5 https://github.com/galaxyproject/galaxy/commit/ade8844d11aa90a1ccda20545d62… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M lib/galaxy/datatypes/binary.py Log Message: ----------- Merge pull request #4279 from ashvark/preview_bam Display preview feature for Bam datatype Compare: https://github.com/galaxyproject/galaxy/compare/14360d6737fb...ade8844d11aa

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[galaxyproject/usegalaxy-playbook] f0726c: drop ismb and gcc from carousel
by GitHub 02 Aug '17

02 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f0726c237e5c660b3f893111e0ef8e4768b9ebc4 https://github.com/galaxyproject/usegalaxy-playbook/commit/f0726c237e5c660b… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M env/common/templates/galaxy/static/welcome.html.j2 Log Message: ----------- drop ismb and gcc from carousel

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[galaxyproject/galaxy] 6d3b11: Moving show workflows in tools panel feature to wo...
by GitHub 02 Aug '17

02 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6d3b11f3e76f8a9c4cde96b5a1ad0d5fca405edf https://github.com/galaxyproject/galaxy/commit/6d3b11f3e76f8a9c4cde96b5a1ad… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Moving show workflows in tools panel feature to workflow main view Commit: 8010cd351da006654e2eee2b124bc10c2e43017a https://github.com/galaxyproject/galaxy/commit/8010cd351da006654e2eee2b124b… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/style/blue/base.css Log Message: ----------- Removing the view for configure workflow menu Commit: 33cc830fb11f9eeee5ecaac39518869de09d7c7a https://github.com/galaxyproject/galaxy/commit/33cc830fb11f9eeee5ecaac39518… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Adding comments Commit: 60aa8e0caf87c4b4c90ea499277af4d08c3c6b93 https://github.com/galaxyproject/galaxy/commit/60aa8e0caf87c4b4c90ea499277a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into workflow_configure_menu Commit: 02c40bbcbe644f03ba5ea3b83d33bde895fb58e5 https://github.com/galaxyproject/galaxy/commit/02c40bbcbe644f03ba5ea3b83d33… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M static/maps/mvc/workflow/workflow.js.map M static/maps/nls/fr/locale.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js M static/scripts/nls/fr/locale.js Log Message: ----------- Fix review comments: removing self from multiple places and correct '>' Commit: ec4d6c0c56e9722db28800c54e0e0a5127330bdf https://github.com/galaxyproject/galaxy/commit/ec4d6c0c56e9722db28800c54e0e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow.js M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow.js Log Message: ----------- Removing the unencoded workflow id from the api and UI Commit: 5eb61b689b70b21a1e3f603a206b0fd5731510be https://github.com/galaxyproject/galaxy/commit/5eb61b689b70b21a1e3f603a206b… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/jobs/runners/cli.py R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/workflow/modules.py A lib/tool_shed/util/admin_util.py Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into workflow_configure_menu Commit: 826f53d8ad4171c86cc81755f219ae0d4e65971f https://github.com/galaxyproject/galaxy/commit/826f53d8ad4171c86cc81755f219… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/mvc/user/user-preferences.js M static/maps/mvc/user/user-preferences.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js Log Message: ----------- Removing the configure menu link from user preferences Commit: 7fe464c821ba9ef3c94f054a6545f938f5d05a52 https://github.com/galaxyproject/galaxy/commit/7fe464c821ba9ef3c94f054a6545… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/model/metadata.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js R templates/webapps/galaxy/dataset/edit_attributes.mako Log Message: ----------- Merge with dev Commit: 324ec35c86c7444b628e301affe1d918f1a2d71f https://github.com/galaxyproject/galaxy/commit/324ec35c86c7444b628e301affe1… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py Log Message: ----------- Restoring the get configure menu api and decode ids Commit: 14360d6737fb3bf42264454939f179ea26fe902c https://github.com/galaxyproject/galaxy/commit/14360d6737fb3bf42264454939f1… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/user/user-preferences.js R client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css Log Message: ----------- Merge pull request #4353 from bgruening/workflow_configure_menu Merging configure menu with main workflow view Compare: https://github.com/galaxyproject/galaxy/compare/f41d2ba8ecf6...14360d6737fb

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[galaxyproject/galaxy] 27e7da: Fix bug: 4247 in search overlay
by GitHub 02 Aug '17

02 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 27e7da9406486fc2a7d40c36332e480d84aab407 https://github.com/galaxyproject/galaxy/commit/27e7da9406486fc2a7d40c36332e… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix bug: 4247 in search overlay Commit: 1e18e6b0795c303172c21c038cd145ef75b51720 https://github.com/galaxyproject/galaxy/commit/1e18e6b0795c303172c21c038cd1… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/model/mapping.py Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into searchoverlay_bugfix Commit: bcecec0713e6778ab6850320943ad12b5f184f16 https://github.com/galaxyproject/galaxy/commit/bcecec0713e6778ab6850320943a… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/nls/fr/locale.js M config/tool_shed.ini.sample M lib/galaxy/jobs/runners/cli.py M lib/galaxy/model/metadata.py M lib/galaxy/security/__init__.py M lib/galaxy/tools/deps/conda_util.py R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/galaxy/workflow/modules.py A lib/tool_shed/util/admin_util.py A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/nls/fr/locale.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/nls/fr/locale.js R templates/webapps/galaxy/dataset/edit_attributes.mako Log Message: ----------- Merge with dev Commit: f41d2ba8ecf6440901fd1106b6bafa6377098ad9 https://github.com/galaxyproject/galaxy/commit/f41d2ba8ecf6440901fd1106b6ba… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M config/plugins/webhooks/demo/search/static/script.js Log Message: ----------- Merge pull request #4348 from bgruening/searchoverlay_bugfix Search Overlay plugin bug fix Compare: https://github.com/galaxyproject/galaxy/compare/98292a0a124a...f41d2ba8ecf6

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[galaxyproject/usegalaxy-playbook] 0a1838: Run unicycler on Bridges
by GitHub 02 Aug '17

02 Aug '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0a1838527f6a1a7cb98f6e13ee12d1317726f813 https://github.com/galaxyproject/usegalaxy-playbook/commit/0a1838527f6a1a7c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M env/test/templates/galaxy/config/job_conf.xml.j2 Log Message: ----------- Run unicycler on Bridges Commit: aafd5807943b509fb8c32b6c16a199c4d844fba3 https://github.com/galaxyproject/usegalaxy-playbook/commit/aafd5807943b509f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-08-02 (Wed, 02 Aug 2017) Changed paths: M env/test/files/galaxy/var/integrated_tool_panel.xml M env/test/files/galaxy/var/shed_tool_conf.xml Log Message: ----------- Test mutable configs Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/3ea4cacef518...…

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[galaxyproject/galaxy] 81af55: Delete conda_exec_home instead of env['HOME']
by GitHub 01 Aug '17

01 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 81af55cfea7853b177782c3d6550b0c62b5d7446 https://github.com/galaxyproject/galaxy/commit/81af55cfea7853b177782c3d6550… Author: mvdbeek <m.vandenbeek(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Delete conda_exec_home instead of env['HOME'] This should always be the same in the current code, but this feels a little safer, given that env is mutable. Commit: 98292a0a124a106bde64dd977f0e505e599ff864 https://github.com/galaxyproject/galaxy/commit/98292a0a124a106bde64dd977f0e… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #4360 from mvdbeek/shutil_rmtree_headache Delete conda_exec_home instead of env['HOME'] Compare: https://github.com/galaxyproject/galaxy/compare/bd0f804085bf...98292a0a124a

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[galaxyproject/galaxy] e7f971: Set up scripts for removing edit attributes mako o...
by GitHub 01 Aug '17

01 Aug '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e7f9714a29893177f479270f7017aec3a976d6df https://github.com/galaxyproject/galaxy/commit/e7f9714a29893177f479270f7017… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/webapps/galaxy/buildapp.py A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js Log Message: ----------- Set up scripts for removing edit attributes mako of Dataset edit action Commit: 6a493ac3001cb0e3345355025ca4a79008ec8d36 https://github.com/galaxyproject/galaxy/commit/6a493ac3001cb0e3345355025ca4… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-10 (Mon, 10 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adding tabs for different sections of edit dataset attributes view Commit: 19ede9b477f8c32d6915152869e73959dc10677c https://github.com/galaxyproject/galaxy/commit/19ede9b477f8c32d6915152869e7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Updating edit attributes view Commit: 5e59549ddf47d12ed03326a65d5858a9d9ec030c https://github.com/galaxyproject/galaxy/commit/5e59549ddf47d12ed03326a65d58… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adding messages to the actions Commit: 95032151fa56681148529eba2d27140db80b7c98 https://github.com/galaxyproject/galaxy/commit/95032151fa56681148529eba2d27… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adding Convert tab to Dataset Edit Attributes page Commit: b3ae53c1e7f8de207aabeb55d96526be07c29752 https://github.com/galaxyproject/galaxy/commit/b3ae53c1e7f8de207aabeb55d965… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-11 (Tue, 11 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Updating logic for extra fields like comments lines Commit: 7ba4f22b61aa248383d99dc2caf1ec747299539a https://github.com/galaxyproject/galaxy/commit/7ba4f22b61aa248383d99dc2caf1… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-16 (Sun, 16 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adding form builder for edit attributes tabs Commit: 3572bad66fd4b1d3899378d5493975c43751c67b https://github.com/galaxyproject/galaxy/commit/3572bad66fd4b1d3899378d54939… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Adding permissions tab Commit: 69934d9f02787a66082a6841e39406198905c936 https://github.com/galaxyproject/galaxy/commit/69934d9f02787a66082a6841e394… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/galaxy.pages.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/dataset/data.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/grid/grid-model.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/nls/ja/locale.js M client/galaxy/scripts/nls/locale.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/phyloviz.js M client/galaxy/scripts/viz/trackster.js M client/galaxy/scripts/viz/trackster/tracks.js M client/galaxy/scripts/viz/visualization.js A client/package-lock.json M config/galaxy.ini.sample M config/tool_conf.xml.main M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/jobs/actions/post.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py A lib/galaxy/objectstore/pithos.py M lib/galaxy/tools/data/__init__.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M scripts/runtime_stats.py M static/maps/galaxy.pages.js.map M static/maps/layout/menu.js.map M static/maps/layout/scratchbook.js.map M static/maps/mvc/dataset/data.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/grid/grid-model.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/nls/ja/locale.js.map M static/maps/nls/locale.js.map M static/maps/viz/circster.js.map M static/maps/viz/phyloviz.js.map M static/maps/viz/trackster.js.map M static/maps/viz/trackster/tracks.js.map M static/maps/viz/visualization.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/galaxy.pages.js M static/scripts/layout/menu.js M static/scripts/layout/scratchbook.js M static/scripts/mvc/dataset/data.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/grid/grid-view.js M static/scripts/nls/ja/locale.js M static/scripts/nls/locale.js M static/scripts/viz/circster.js M static/scripts/viz/phyloviz.js M static/scripts/viz/trackster.js M static/scripts/viz/trackster/tracks.js M static/scripts/viz/visualization.js R templates/webapps/galaxy/history/list_published.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/select_items_grid.mako R templates/webapps/galaxy/tracks/add_to_viz.mako R templates/webapps/galaxy/tracks/add_tracks.mako R templates/webapps/galaxy/tracks/history_datasets_select_grid.mako R templates/webapps/galaxy/tracks/history_select_grid.mako R templates/webapps/galaxy/tracks/library_datasets_select_grid.mako Log Message: ----------- Merging with dev Commit: 9604fb3844bcf936bd73581d7adefabd7f99f491 https://github.com/galaxyproject/galaxy/commit/9604fb3844bcf936bd73581d7ade… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Resolve the save permission issue Commit: 44d24c39f7873ea86d21d56c15565f041fbaab20 https://github.com/galaxyproject/galaxy/commit/44d24c39f7873ea86d21d56c1556… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-17 (Mon, 17 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Add form builder for the attributes tab Commit: 212ffc7476551568136391e9bfd2c34d84269731 https://github.com/galaxyproject/galaxy/commit/212ffc7476551568136391e9bfd2… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/model/metadata.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Add metadata fields Commit: 90247d7432ac7942797a574c3e241316d18f5bcf https://github.com/galaxyproject/galaxy/commit/90247d7432ac7942797a574c3e24… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/model/metadata.py M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Build inputs in controller Commit: 9853625e905c14fd9b9fd706a0c7a174da9135e0 https://github.com/galaxyproject/galaxy/commit/9853625e905c14fd9b9fd706a0c7… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js A client/galaxy/scripts/mvc/grid/grid-shared.js R client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/viz/circster.js M client/galaxy/scripts/viz/trackster.js M client/package-lock.json A config/plugins/visualizations/unipept/README.md A config/plugins/visualizations/unipept/config/unipept.xml A config/plugins/visualizations/unipept/static/style.css A config/plugins/visualizations/unipept/static/tooltip.css A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js A config/plugins/visualizations/unipept/static/unipept-visualizations.es5.js.map A config/plugins/visualizations/unipept/static/unipept_viz.js A config/plugins/visualizations/unipept/templates/glyphicons-86-repeat.png A config/plugins/visualizations/unipept/templates/unipept.mako M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M static/maps/layout/menu.js.map A static/maps/mvc/grid/grid-shared.js.map R static/maps/mvc/page/page-list.js.map M static/maps/viz/circster.js.map M static/maps/viz/trackster.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js A static/scripts/mvc/grid/grid-shared.js R static/scripts/mvc/page/page-list.js M static/scripts/viz/circster.js M static/scripts/viz/trackster.js M templates/webapps/galaxy/requests/common/common.mako R templates/webapps/galaxy/visualization/list.mako Log Message: ----------- Merge with def Commit: 9c83253c41645ec253e8320604c9b9ae5254412c https://github.com/galaxyproject/galaxy/commit/9c83253c41645ec253e8320604c9… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Changes for setting values of select box in metadata Commit: ac6ad5aabac9ca34baf8d0ebede25073e2fa7bae https://github.com/galaxyproject/galaxy/commit/ac6ad5aabac9ca34baf8d0ebede2… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Update the help text Commit: a302dee11e4f66244992655c51dbf8affa1a88e8 https://github.com/galaxyproject/galaxy/commit/a302dee11e4f66244992655c51db… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Correct the indentations and spacings Commit: f4ffef05ce501f8f40efb4461c678d7a3b1ca01d https://github.com/galaxyproject/galaxy/commit/f4ffef05ce501f8f40efb4461c67… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: R templates/webapps/galaxy/dataset/edit_attributes.mako Log Message: ----------- Removing the edit attributes mako file Commit: 315fd58fcac02097efc42dac7e2db68fa6bd6db3 https://github.com/galaxyproject/galaxy/commit/315fd58fcac02097efc42dac7e2d… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-23 (Sun, 23 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Fixing build fail comments Commit: 8fa3b2b97a07c2b9a6c015aec56445c2d049bfd0 https://github.com/galaxyproject/galaxy/commit/8fa3b2b97a07c2b9a6c015aec564… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-25 (Tue, 25 Jul 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M lib/galaxy/webapps/galaxy/controllers/dataset.py M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Fixing PR review comments Commit: f8e6fcaebc8b7968daba841fd172636bf37e3858 https://github.com/galaxyproject/galaxy/commit/f8e6fcaebc8b7968daba841fd172… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-edit-attributes.js Log Message: ----------- Removing unsued self vars and using just Backbone.Model Commit: 2f5b26e8b6dcb47b5ca69466b6510fa58bea1f7c https://github.com/galaxyproject/galaxy/commit/2f5b26e8b6dcb47b5ca69466b651… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-30 (Sun, 30 Jul 2017) Changed paths: M client/galaxy/scripts/nls/fr/locale.js M config/tool_shed.ini.sample M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/jobs/runners/cli.py M lib/galaxy/model/mapping.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge branch 'dev' of https://github.com/bgruening/galaxy into edit_attributes_mako Commit: 8502a6854a363eca1f8180e25f11f322d4a094f4 https://github.com/galaxyproject/galaxy/commit/8502a6854a363eca1f8180e25f11… Author: anuprulez <anup.rulez(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/nls/fr/locale.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/nls/fr/locale.js Log Message: ----------- Updating the dataset id Commit: bd0f804085bf1fa467001554dd8e51ad999aa261 https://github.com/galaxyproject/galaxy/commit/bd0f804085bf1fa467001554dd8e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-08-01 (Tue, 01 Aug 2017) Changed paths: M client/galaxy/scripts/apps/analysis.js A client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M lib/galaxy/model/metadata.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py A static/maps/mvc/dataset/dataset-edit-attributes.js.map M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/nls/fr/locale.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map A static/scripts/mvc/dataset/dataset-edit-attributes.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/nls/fr/locale.js R templates/webapps/galaxy/dataset/edit_attributes.mako Log Message: ----------- Merge pull request #4334 from bgruening/edit_attributes_mako Replacing Edit Attributes Mako by JavaScript Compare: https://github.com/galaxyproject/galaxy/compare/2659718a6d71...bd0f804085bf

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[galaxyproject/galaxy] 268186: Replicate admin controller for toolshed
by GitHub 31 Jul '17

31 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 268186a0d98927d090796c8e5ce21646083d1787 https://github.com/galaxyproject/galaxy/commit/268186a0d98927d090796c8e5ce2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: A lib/tool_shed/util/admin_util.py Log Message: ----------- Replicate admin controller for toolshed Commit: 3cc654836946f0061af4b69130b2b89c79f361b7 https://github.com/galaxyproject/galaxy/commit/3cc654836946f0061af4b69130b2… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Remove repository_util dependency Commit: b4506e2a347cb4fbf4becffff2870bfd7277a2c6 https://github.com/galaxyproject/galaxy/commit/b4506e2a347cb4fbf4becffff287… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Link to toolshed specific controller Commit: 94391305d8c55fbcb43ab517dad5e2681e08259c https://github.com/galaxyproject/galaxy/commit/94391305d8c55fbcb43ab517dad5… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Insert admin base controller endpoints into galaxy admin controller Commit: 6a8841189d51b89da2c9be098440bd0002a6ecb7 https://github.com/galaxyproject/galaxy/commit/6a8841189d51b89da2c9be098440… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py Log Message: ----------- Remove base admin controller Commit: 2f79e00649aa1863d53d3149c6b1a2e5981a5cc5 https://github.com/galaxyproject/galaxy/commit/2f79e00649aa1863d53d3149c6b1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Transfer non-overlapping dependencies Commit: 616c0326fcd60120e4d4f6d0171fededf48f4c72 https://github.com/galaxyproject/galaxy/commit/616c0326fcd60120e4d4f6d0171f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py Log Message: ----------- Remove redundant dependency Commit: 39cce1abb20ace8f4e988fbb3426476e33cc883b https://github.com/galaxyproject/galaxy/commit/39cce1abb20ace8f4e988fbb3426… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Add new line Commit: 97a4cb9686c260d233e01e08861f0481b63ac670 https://github.com/galaxyproject/galaxy/commit/97a4cb9686c260d233e01e08861f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Avoid inheriting the admin controller for quota api Commit: 917d2d98b42da1561bef1773f1f94ac8f3df8496 https://github.com/galaxyproject/galaxy/commit/917d2d98b42da1561bef1773f1f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Remove endpoints not needed in toolshed Commit: 7a0c041bc251ea9b122db2adf887db25633e964a https://github.com/galaxyproject/galaxy/commit/7a0c041bc251ea9b122db2adf887… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/tool_shed/util/admin_util.py Log Message: ----------- Remove unused utility functions of controller Commit: e85b3f9951738ed3229ff00a5ed718a916b5c598 https://github.com/galaxyproject/galaxy/commit/e85b3f9951738ed3229ff00a5ed7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-20 (Thu, 20 Jul 2017) Changed paths: M lib/tool_shed/util/admin_util.py Log Message: ----------- Remove unused dependencies Commit: 36cd79b535b98520116a6531dedaf05b15c11c93 https://github.com/galaxyproject/galaxy/commit/36cd79b535b98520116a6531deda… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Remove unused method Commit: 2659718a6d71d89a07a8440a000e2e7b86cf64e6 https://github.com/galaxyproject/galaxy/commit/2659718a6d71d89a07a8440a000e… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: R lib/galaxy/web/base/controllers/__init__.py R lib/galaxy/web/base/controllers/admin.py M lib/galaxy/webapps/galaxy/api/quotas.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/tool_shed/controllers/admin.py A lib/tool_shed/util/admin_util.py Log Message: ----------- Merge pull request #4327 from guerler/separate_admin_controllers Separate admin controllers Compare: https://github.com/galaxyproject/galaxy/compare/79b1ad601118...2659718a6d71

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[galaxyproject/infrastructure-playbook]
by GitHub 31 Jul '17

31 Jul '17

Branch: refs/heads/https-include Home: https://github.com/galaxyproject/infrastructure-playbook

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[galaxyproject/infrastructure-playbook] d83c1a: include https in training redirect
by GitHub 31 Jul '17

31 Jul '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d83c1a7eefa7ea16fbe3b1960efdcd2257271f8c https://github.com/galaxyproject/infrastructure-playbook/commit/d83c1a7eefa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M galaxyenv/templates/nginx/training.j2 Log Message: ----------- include https in training redirect Commit: 7d295c71010067a4e9e9e3831e2cfafaa2b2b228 https://github.com/galaxyproject/infrastructure-playbook/commit/7d295c71010… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M galaxyenv/templates/nginx/training.j2 Log Message: ----------- Merge pull request #18 from galaxyproject/https-include include https in training redirect Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/91921fe770…

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[galaxyproject/infrastructure-playbook] d83c1a: include https in training redirect
by GitHub 31 Jul '17

31 Jul '17

Branch: refs/heads/https-include Home: https://github.com/galaxyproject/infrastructure-playbook Commit: d83c1a7eefa7ea16fbe3b1960efdcd2257271f8c https://github.com/galaxyproject/infrastructure-playbook/commit/d83c1a7eefa… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M galaxyenv/templates/nginx/training.j2 Log Message: ----------- include https in training redirect

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[galaxyproject/galaxy] 12f0ac: Revert "Revert "[release_17.05] Patch bug preventi...
by GitHub 31 Jul '17

31 Jul '17

Branch: refs/heads/release_17.05 Home: https://github.com/galaxyproject/galaxy Commit: 12f0acba1dc1b81bb621ea130a75ec7dfac0fdaa https://github.com/galaxyproject/galaxy/commit/12f0acba1dc1b81bb621ea130a75… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Revert "Revert "[release_17.05] Patch bug preventing creation of dataset library folders"" Commit: 10efd7fac6e38c5ca07d94c351d10473811c7d6c https://github.com/galaxyproject/galaxy/commit/10efd7fac6e38c5ca07d94c351d1… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-07-31 (Mon, 31 Jul 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js A static/maps/mvc/job/job-params.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map A static/scripts/mvc/job/job-params.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #4357 from galaxyproject/revert-4356-revert-4355-patch-wrong-folder-id [release_17.05] Patch bug preventing creation of dataset library folders Compare: https://github.com/galaxyproject/galaxy/compare/163e4ebbe1fb...10efd7fac6e3

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[galaxyproject/galaxy] 092626: Remove print debug option from toolshed.
by GitHub 28 Jul '17

28 Jul '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0926266cbea49a0f30ebeb22cb0a0a95843d7187 https://github.com/galaxyproject/galaxy/commit/0926266cbea49a0f30ebeb22cb0a… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2017-07-21 (Fri, 21 Jul 2017) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Remove print debug option from toolshed. After investigating, I've determined that it's not worth the effort to fix the print debug middleware, so this will remove the option from buildapp.py and tool_shed.ini.sample Commit: 8923912c89c7ada8a9ad7d1a2533eb44d17a9e36 https://github.com/galaxyproject/galaxy/commit/8923912c89c7ada8a9ad7d1a2533… Author: Dave B <dave(a)bx.psu.edu> Date: 2017-07-27 (Thu, 27 Jul 2017) Changed paths: M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Fix logic. Commit: 79b1ad6011182075f4a7648f72f3fa7bb5d8fd6f https://github.com/galaxyproject/galaxy/commit/79b1ad6011182075f4a7648f72f3… Author: Eric Rasche <hxr(a)hx42.org> Date: 2017-07-28 (Fri, 28 Jul 2017) Changed paths: M config/tool_shed.ini.sample M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Merge pull request #4332 from davebx/remove_printdebug Remove print debug option from toolshed. Compare: https://github.com/galaxyproject/galaxy/compare/e1c54f37d904...79b1ad601118

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