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[galaxyproject/galaxy] f64d15: Extension point for environment variables.
by GitHub 03 Dec '15

03 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f64d1597b84801dd48c2cdb5bc0c303355786942 https://github.com/galaxyproject/galaxy/commit/f64d1597b84801dd48c2cdb5bc0c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Extension point for environment variables. Commit: ea9f4a0467b6955ccc470da06eaf7c13e7643715 https://github.com/galaxyproject/galaxy/commit/ea9f4a0467b6955ccc470da06eaf… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Initialize a ToolOutput.from_work_dir. Commit: 7ce43a0463c3d98b757d78d0600aadf5d7876eb9 https://github.com/galaxyproject/galaxy/commit/7ce43a0463c3d98b757d78d0600a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/workflow/run_request.py Log Message: ----------- Refactor run_request for downstream diff improvements. Commit: 77ed5681f8565b12ab1d5e5c7d0302c938e9c73d https://github.com/galaxyproject/galaxy/commit/77ed5681f8565b12ab1d5e5c7d03… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Extend base api workflow _run_jobs helper... ... to allow loading content from test-data files. Commit: 42778e27539d919ff11d67a07368c0b6e4ebae75 https://github.com/galaxyproject/galaxy/commit/42778e27539d919ff11d67a07368… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/workflow/run.py Log Message: ----------- Improved error handling in workflow run code. Commit: 28501ab676f9df797bae316c3d24e9ae8fd58a9b https://github.com/galaxyproject/galaxy/commit/28501ab676f9df797bae316c3d24… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M test/unit/test_galaxy_mapping.py Log Message: ----------- Refactor workflow manager for extension. Commit: 4584a579a297ffd02bd77584b71a8c17d85d261a https://github.com/galaxyproject/galaxy/commit/4584a579a297ffd02bd77584b71a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Fix interface declaration for WorkflowModule.get_state. Implementers all take this attribute. Commit: 21213ef70f535e06bc485370686807a6d2850345 https://github.com/galaxyproject/galaxy/commit/21213ef70f535e06bc4853706868… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_render.py M test/unit/workflows/workflow_support.py Log Message: ----------- Refactor workflow testing code to quickly bootstrap workflows. Commit: 031a39aba83932fd0291f440a7e58c962deadfe8 https://github.com/galaxyproject/galaxy/commit/031a39aba83932fd0291f440a7e5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Basic unit tests for workflow progress tracking. Commit: 8a01b42112ec32e5f978f3a4245127cad3219c45 https://github.com/galaxyproject/galaxy/commit/8a01b42112ec32e5f978f3a42451… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/model/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Refactor input_by_connections_name logic into model. Continue to delay calculation of this but auto-compute it if requested and module injection code hasn't been called explicitly. Moves logic internal to class where it belongs also. Commit: cf367ff0c75454837359b74046c05cc7cb456dc5 https://github.com/galaxyproject/galaxy/commit/cf367ff0c75454837359b74046c0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Add another workflow progress test case. This one for replacing a tool input with an input dataset. Commit: 7974c1f33486c0a66803004c5d7885a9d91b9c70 https://github.com/galaxyproject/galaxy/commit/7974c1f33486c0a66803004c5d78… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Add unit tests for workflow progress initialization. Commit: 07c3d10f31e48f783baf05c133b117e7f3e7ee1a https://github.com/galaxyproject/galaxy/commit/07c3d10f31e48f783baf05c133b1… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Extend workflow recovery progress test case to include replacement check. Commit: 48340b5829fb5ca346060d9372ba7df7e3effcef https://github.com/galaxyproject/galaxy/commit/48340b5829fb5ca346060d9372ba… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M test/unit/workflows/test_workflow_progress.py Log Message: ----------- Add TODO items to workflow progress unit tests. Commit: dd5f3aec52d1cec8e2a98dc9cf7134cd9b381d84 https://github.com/galaxyproject/galaxy/commit/dd5f3aec52d1cec8e2a98dc9cf71… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix workflow extraction test cases broken with 77ed5681f8565b12ab1d5e5c7d0302c938e9c73d Commit: 20b96d883d9ef33b51d5a32d82ce2d1251daf572 https://github.com/galaxyproject/galaxy/commit/20b96d883d9ef33b51d5a32d82ce… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-12-03 (Thu, 03 Dec 2015) Changed paths: M lib/galaxy/managers/workflows.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/run_request.py M test/api/test_workflows.py M test/unit/test_galaxy_mapping.py M test/unit/workflows/test_render.py A test/unit/workflows/test_workflow_progress.py M test/unit/workflows/workflow_support.py Log Message: ----------- Merge pull request #1202 from jmchilton/workflow_tool_refactoring Small Tool and Workflow Refactoring and Fixes Compare: https://github.com/galaxyproject/galaxy/compare/ffb3de9ede51...20b96d883d9e

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[galaxyproject/galaxy] 51cd41: Fix ScIdx sniff method to handle first line commen...
by GitHub 02 Dec '15

02 Dec '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 51cd41be94ea4e5af50201bbd0e85ade21774e69 https://github.com/galaxyproject/galaxy/commit/51cd41be94ea4e5af50201bbd0e8… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Fix ScIdx sniff method to handle first line comment Commit: c04b3a5bb557c836e60c060f68598ea314fc9521 https://github.com/galaxyproject/galaxy/commit/c04b3a5bb557c836e60c060f6859… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Re-add egg imports Commit: 30b13bb1d6e576c4f6e32f4e98b08c9a3a5651eb https://github.com/galaxyproject/galaxy/commit/30b13bb1d6e576c4f6e32f4e98b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1203 from gregvonkuster/release_15.10 [15.10] Fix ScIdx sniff method to handle first line comment Compare: https://github.com/galaxyproject/galaxy/compare/da2cc588e5a5...30b13bb1d6e5

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[galaxyproject/usegalaxy-playbook] d26b97: change Main config; allow importing from FTP folde...
by GitHub 02 Dec '15

02 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d26b9739c642d53ef9c88cc7f24d4bca9c3140c5 https://github.com/galaxyproject/usegalaxy-playbook/commit/d26b9739c642d53e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M production/group_vars/galaxyservers.yml Log Message: ----------- change Main config; allow importing from FTP folder to datalibs

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[galaxyproject/galaxy] 0c22d1: Implement type_source on output collections.
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0c22d138891604d0df98784ab7edc43e9b541c1d https://github.com/galaxyproject/galaxy/commit/0c22d138891604d0df98784ab7ed… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-20 (Fri, 20 Nov 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/xml.py A test/functional/tools/collection_type_source.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement type_source on output collections. Inherit collection_type from an input, the way metadata and format can be. This commit includes a test tool demonstrating this functionality. The tool test for this tool can be executed using the following command: ``` ./run_tests.sh -framework -id collection_type_source ``` Commit: ffb3de9ede515d10fbdf06519140a726e0cfa7d1 https://github.com/galaxyproject/galaxy/commit/ffb3de9ede515d10fbdf06519140… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-12-02 (Wed, 02 Dec 2015) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parser/xml.py A test/functional/tools/collection_type_source.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1153 from jmchilton/collection_type_source Implement type_source on output collections. Compare: https://github.com/galaxyproject/galaxy/compare/67c98f54cad4...ffb3de9ede51

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[galaxyproject/galaxy] ff619d: Downgrade Mercurial wheel to 3.4.2 to restore hg p...
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ff619df3946621b819df03909fc63ce9ee412ced https://github.com/galaxyproject/galaxy/commit/ff619df3946621b819df03909fc6… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt M lib/tool_shed/util/hg_util.py Log Message: ----------- Downgrade Mercurial wheel to 3.4.2 to restore hg push of Tool Shed repositories. Fix #1183. Commit: 657afa89d3ac91e53a84ae132334f137eb07acdc https://github.com/galaxyproject/galaxy/commit/657afa89d3ac91e53a84ae132334… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/tool_shed/util/common_util.py Log Message: ----------- Small fixes. Commit: 194d871e38b3815bba120d6bb40c3eef45660738 https://github.com/galaxyproject/galaxy/commit/194d871e38b3815bba120d6bb40c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/tool_shed/util/hg_util.py Log Message: ----------- Fix Tool Shed export capsule for Mercurial >= 3.4 . Fix the following error: tool_shed.capsule.capsule_manager ERROR 2015-12-01 12:24:37,542 unable to find mercurial command "archive" Traceback (most recent call last): File "/opt/galaxy/lib/tool_shed/capsule/capsule_manager.py", line 88, in export_repository work_dir ) File "/opt/galaxy/lib/tool_shed/capsule/capsule_manager.py", line 148, in generate_repository_archive changeset_revision ) File "/opt/galaxy/lib/tool_shed/util/hg_util.py", line 28, in archive_repository_revision options_dict = get_mercurial_default_options_dict( 'archive' ) File "/opt/galaxy/lib/tool_shed/util/hg_util.py", line 200, in get_mercurial_default_options_dict raise Exception('unable to find mercurial command "%s"' % command) Exception: unable to find mercurial command "archive" Commit: 67c98f54cad4f20413568417e2cbb97bee24b0e5 https://github.com/galaxyproject/galaxy/commit/67c98f54cad4f20413568417e2cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py Log Message: ----------- Merge pull request #1200 from nsoranzo/tool_shed_fixes Tool shed fixes. Compare: https://github.com/galaxyproject/galaxy/compare/84464288b18c...67c98f54cad4

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[galaxyproject/usegalaxy-playbook] 7f140f: Update GCC2016 redirect
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7f140f63d6095f01123da96fe6aed62f529c0614 https://github.com/galaxyproject/usegalaxy-playbook/commit/7f140f63d6095f01… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M templates/nginx/galaxyproject.j2 Log Message: ----------- Update GCC2016 redirect

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[galaxyproject/infrastructure-playbook] 8597fd: Allow jenkins to log in to mjolnir0 for building w...
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 8597fdb06f69c4b0cade4b9e8f363aebe3c67704 https://github.com/galaxyproject/infrastructure-playbook/commit/8597fdb06f6… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M galaxyenv/group_vars/starforgebuilders.yml M galaxyenv/secret_group_vars/all.yml M galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml M galaxyenv/secret_host_vars/mjolnir0.galaxyproject.org.yml Log Message: ----------- Allow jenkins to log in to mjolnir0 for building wheels

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[galaxyproject/infrastructure-playbook] 843efb: Update common roles
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 843efba2e84bcdf907c267488e62d697e8a5d5e1 https://github.com/galaxyproject/infrastructure-playbook/commit/843efba2e84… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M common_roles Log Message: ----------- Update common roles

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[galaxyproject/galaxy] 2e9755: Filter download links
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2e97553194a0e13dc4158c29a161c0b678bcd02e https://github.com/galaxyproject/galaxy/commit/2e97553194a0e13dc4158c29a161… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-28 (Sat, 28 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.frame.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/galaxy.frame.js.map M static/maps/galaxy.masthead.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/galaxy.frame.js M static/scripts/galaxy.masthead.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Filter download links Commit: 84464288b18ca587334dba89c9fd011c7f3a0fc6 https://github.com/galaxyproject/galaxy/commit/84464288b18ca587334dba89c9fd… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M client/galaxy/scripts/galaxy.frame.js M client/galaxy/scripts/galaxy.masthead.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-buttons.js M static/maps/galaxy.frame.js.map M static/maps/galaxy.masthead.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-buttons.js.map M static/scripts/galaxy.frame.js M static/scripts/galaxy.masthead.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-buttons.js Log Message: ----------- Merge pull request #1184 from guerler/fix_download_links_002 Filter download links, avoid warning dialog Compare: https://github.com/galaxyproject/galaxy/compare/3524476bc6c7...84464288b18c

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[galaxyproject/galaxy] 5bd898: deprecate TS direct hg api
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5bd898118f96ff30093fcd932de3483fee028453 https://github.com/galaxyproject/galaxy/commit/5bd898118f96ff30093fcd932de3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- deprecate TS direct hg api Commit: da2cc588e5a5c4ee528ad1c6e406fe7837d58e8e https://github.com/galaxyproject/galaxy/commit/da2cc588e5a5c4ee528ad1c6e406… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #1194 from martenson/release_15.10 [15.10] docs - deprecate TS direct hg api Commit: 3524476bc6c75461fd8b793a3bf047d1ad475e2a https://github.com/galaxyproject/galaxy/commit/3524476bc6c75461fd8b793a3bf0… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-12-01 (Tue, 01 Dec 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge branch 'master' into dev Compare: https://github.com/galaxyproject/galaxy/compare/9e28f2e786bc...3524476bc6c7

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[galaxyproject/galaxy] 5bd898: deprecate TS direct hg api
by GitHub 01 Dec '15

01 Dec '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 5bd898118f96ff30093fcd932de3483fee028453 https://github.com/galaxyproject/galaxy/commit/5bd898118f96ff30093fcd932de3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- deprecate TS direct hg api Commit: da2cc588e5a5c4ee528ad1c6e406fe7837d58e8e https://github.com/galaxyproject/galaxy/commit/da2cc588e5a5c4ee528ad1c6e406… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #1194 from martenson/release_15.10 [15.10] docs - deprecate TS direct hg api Compare: https://github.com/galaxyproject/galaxy/compare/a03404c04d41...da2cc588e5a5

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[galaxyproject/usegalaxy-playbook] e73878: update MTS
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e73878d845f6937e17e6902283c45b3f9d3fc0fe https://github.com/galaxyproject/usegalaxy-playbook/commit/e73878d845f6937e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS

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commit/galaxy-central: natefoo: Create branch release_15.10
by commits-noreply＠bitbucket.org 30 Nov '15

30 Nov '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/af33af5cfc6b/ Changeset: af33af5cfc6b Branch: release_15.10 User: natefoo Date: 2015-11-30 19:39:18+00:00 Summary: Create branch release_15.10 Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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[galaxyproject/galaxy] 5bd898: deprecate TS direct hg api
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 5bd898118f96ff30093fcd932de3483fee028453 https://github.com/galaxyproject/galaxy/commit/5bd898118f96ff30093fcd932de3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- deprecate TS direct hg api Commit: da2cc588e5a5c4ee528ad1c6e406fe7837d58e8e https://github.com/galaxyproject/galaxy/commit/da2cc588e5a5c4ee528ad1c6e406… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M doc/source/releases/15.10_announce.rst Log Message: ----------- Merge pull request #1194 from martenson/release_15.10 [15.10] docs - deprecate TS direct hg api Compare: https://github.com/galaxyproject/galaxy/compare/a03404c04d41...da2cc588e5a5

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[galaxyproject/galaxy] 95507c: fix whitespace
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/galaxy Commit: 95507c5d02cd56199c232a8cd829e46c3f43ef7a https://github.com/galaxyproject/galaxy/commit/95507c5d02cd56199c232a8cd829… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- fix whitespace Commit: e142beaffe1ee6aa853bbdb211ccf3fe1beb509e https://github.com/galaxyproject/galaxy/commit/e142beaffe1ee6aa853bbdb211cc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- replace wrong class name Commit: 39bc057ef9d9e62f08e3c0dbdb95d14a1ae295d2 https://github.com/galaxyproject/galaxy/commit/39bc057ef9d9e62f08e3c0dbdb95… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix whitespace Commit: e19b7f656f6750cc87f7d3e7f0eb12d4292d1987 https://github.com/galaxyproject/galaxy/commit/e19b7f656f6750cc87f7d3e7f0eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the extra slash in URL when creating folder Commit: 87b9d1a5f44a6e42397694e16f17c97c504c1b27 https://github.com/galaxyproject/galaxy/commit/87b9d1a5f44a6e42397694e16f17… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-28 (Sat, 28 Nov 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Add support for Strand-specific COordinate Count datatype Commit: 6fdff2d2f88458cef6f29ee3cb8bb895babab62c https://github.com/galaxyproject/galaxy/commit/6fdff2d2f88458cef6f29ee3cb8b… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-28 (Sat, 28 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add Strand-specific Coordinate Count datatype entry to the datatypes config. Commit: 21fad8ac88a46996b2ff2719527709374f0c9913 https://github.com/galaxyproject/galaxy/commit/21fad8ac88a46996b2ff27195277… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Set the column names and edit the comments section Commit: c532f6808efda37be88a0519e3c44ad523541fa9 https://github.com/galaxyproject/galaxy/commit/c532f6808efda37be88a0519e3c4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1186 from gregvonkuster/release_15.10 [15.10] Add support for Strand-specific Coordinate Count datatype Commit: a03404c04d41156dd5f962a72a0ca3913969f14f https://github.com/galaxyproject/galaxy/commit/a03404c04d41156dd5f962a72a0c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1162 from martenson/fix-datalibs [15.10] Fix two bugs in datalibs Compare: https://github.com/galaxyproject/galaxy/compare/a5200a4d5f97...a03404c04d41

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[galaxyproject/galaxy]
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/tags/v15.10 Home: https://github.com/galaxyproject/galaxy

1 0

[galaxyproject/galaxy] 95507c: fix whitespace
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 95507c5d02cd56199c232a8cd829e46c3f43ef7a https://github.com/galaxyproject/galaxy/commit/95507c5d02cd56199c232a8cd829… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- fix whitespace Commit: e142beaffe1ee6aa853bbdb211ccf3fe1beb509e https://github.com/galaxyproject/galaxy/commit/e142beaffe1ee6aa853bbdb211cc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- replace wrong class name Commit: 39bc057ef9d9e62f08e3c0dbdb95d14a1ae295d2 https://github.com/galaxyproject/galaxy/commit/39bc057ef9d9e62f08e3c0dbdb95… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix whitespace Commit: e19b7f656f6750cc87f7d3e7f0eb12d4292d1987 https://github.com/galaxyproject/galaxy/commit/e19b7f656f6750cc87f7d3e7f0eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the extra slash in URL when creating folder Commit: 87b9d1a5f44a6e42397694e16f17c97c504c1b27 https://github.com/galaxyproject/galaxy/commit/87b9d1a5f44a6e42397694e16f17… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-28 (Sat, 28 Nov 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Add support for Strand-specific COordinate Count datatype Commit: 6fdff2d2f88458cef6f29ee3cb8bb895babab62c https://github.com/galaxyproject/galaxy/commit/6fdff2d2f88458cef6f29ee3cb8b… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-28 (Sat, 28 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add Strand-specific Coordinate Count datatype entry to the datatypes config. Commit: 21fad8ac88a46996b2ff2719527709374f0c9913 https://github.com/galaxyproject/galaxy/commit/21fad8ac88a46996b2ff27195277… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Set the column names and edit the comments section Commit: c532f6808efda37be88a0519e3c44ad523541fa9 https://github.com/galaxyproject/galaxy/commit/c532f6808efda37be88a0519e3c4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1186 from gregvonkuster/release_15.10 [15.10] Add support for Strand-specific Coordinate Count datatype Commit: a03404c04d41156dd5f962a72a0ca3913969f14f https://github.com/galaxyproject/galaxy/commit/a03404c04d41156dd5f962a72a0c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1162 from martenson/fix-datalibs [15.10] Fix two bugs in datalibs Commit: 9e28f2e786bcb2bc727f7dba571742f9d2773165 https://github.com/galaxyproject/galaxy/commit/9e28f2e786bcb2bc727f7dba5717… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/interval.py M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge branch 'release_15.10' into dev Compare: https://github.com/galaxyproject/galaxy/compare/492fcdab9fa1...9e28f2e786bc

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[galaxyproject/galaxy] 95507c: fix whitespace
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 95507c5d02cd56199c232a8cd829e46c3f43ef7a https://github.com/galaxyproject/galaxy/commit/95507c5d02cd56199c232a8cd829… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- fix whitespace Commit: e142beaffe1ee6aa853bbdb211ccf3fe1beb509e https://github.com/galaxyproject/galaxy/commit/e142beaffe1ee6aa853bbdb211cc… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/scripts/mvc/library/library-folderrow-view.js Log Message: ----------- replace wrong class name Commit: 39bc057ef9d9e62f08e3c0dbdb95d14a1ae295d2 https://github.com/galaxyproject/galaxy/commit/39bc057ef9d9e62f08e3c0dbdb95… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix whitespace Commit: e19b7f656f6750cc87f7d3e7f0eb12d4292d1987 https://github.com/galaxyproject/galaxy/commit/e19b7f656f6750cc87f7d3e7f0eb… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-23 (Mon, 23 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- fix the extra slash in URL when creating folder Commit: a03404c04d41156dd5f962a72a0ca3913969f14f https://github.com/galaxyproject/galaxy/commit/a03404c04d41156dd5f962a72a0c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/library/library-folderrow-view.js M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js M static/maps/mvc/library/library-folderrow-view.js.map M static/maps/mvc/library/library-foldertoolbar-view.js.map M static/scripts/mvc/library/library-folderrow-view.js M static/scripts/mvc/library/library-foldertoolbar-view.js Log Message: ----------- Merge pull request #1162 from martenson/fix-datalibs [15.10] Fix two bugs in datalibs Compare: https://github.com/galaxyproject/galaxy/compare/c532f6808efd...a03404c04d41

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[galaxyproject/galaxy] 87b9d1: Add support for Strand-specific COordinate Count d...
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 87b9d1a5f44a6e42397694e16f17c97c504c1b27 https://github.com/galaxyproject/galaxy/commit/87b9d1a5f44a6e42397694e16f17… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-28 (Sat, 28 Nov 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Add support for Strand-specific COordinate Count datatype Commit: 6fdff2d2f88458cef6f29ee3cb8bb895babab62c https://github.com/galaxyproject/galaxy/commit/6fdff2d2f88458cef6f29ee3cb8b… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-28 (Sat, 28 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample Log Message: ----------- Add Strand-specific Coordinate Count datatype entry to the datatypes config. Commit: 21fad8ac88a46996b2ff2719527709374f0c9913 https://github.com/galaxyproject/galaxy/commit/21fad8ac88a46996b2ff27195277… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/datatypes/interval.py Log Message: ----------- Set the column names and edit the comments section Commit: c532f6808efda37be88a0519e3c44ad523541fa9 https://github.com/galaxyproject/galaxy/commit/c532f6808efda37be88a0519e3c4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/interval.py Log Message: ----------- Merge pull request #1186 from gregvonkuster/release_15.10 [15.10] Add support for Strand-specific Coordinate Count datatype Compare: https://github.com/galaxyproject/galaxy/compare/a5200a4d5f97...c532f6808efd

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[galaxyproject/galaxy] 2829ca: Add enhancements to the Galaxy repository install ...
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2829cab105c202a49904d65d88a9ac37dc12d81e https://github.com/galaxyproject/galaxy/commit/2829cab105c202a49904d65d88a9… Author: Greg Von Kuster <ghv2(a)psu.edu> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Add enhancements to the Galaxy repository install process to cleanly handle the case described here: https://github.com/galaxyproject/galaxy/issues/667. Specifically, the following scenario is now cleanly handled: Example use case: In a toolshed I have a repository of a tool, say package_new_gene_db_1_2_3, and in revision 1 it depends on package_sqlite_1_0_0: package_new_gene_db_1_2_3 package_sqlite_1_0_0 At some point in time I discover that postgres is a better solution for my gene database, and I upload revision 2: package_new_gene_db_1_2_3 package_postgres__2_0_0 And I remove the dependecy of sqlite. If I go to my galaxy instance and I remove revision 1 and install revision 2, the installation is cleanly handled with theis PR. It should be noted that this enhancement could adversely impact reproducibility if best practices are not followed with regard to defining package dependencies. Since it is now cleanly possible to eliminate dependencies over time, best practices must be followed to ensure that elimination of a dependency does not affect the output of a tool that uses the underlying hierarchy of packages. Commit: 492fcdab9fa1cdc1465c191289077e103d8d8020 https://github.com/galaxyproject/galaxy/commit/492fcdab9fa1cdc1465c19128907… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/tool_shed/util/shed_util_common.py Log Message: ----------- Merge pull request #1193 from mvdbeek/gvk_ts_fixes Add enhancements to the Galaxy repository install process Compare: https://github.com/galaxyproject/galaxy/compare/f35bd9ae02aa...492fcdab9fa1

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[galaxyproject/galaxy] 2568e8: Renames reports_wsgi.ini
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2568e85e7b84a8d9c7039f4c4b44661b9930a55e https://github.com/galaxyproject/galaxy/commit/2568e85e7b84a8d9c7039f4c4b44… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: A config/reports.ini.sample R config/reports_wsgi.ini.sample Log Message: ----------- Renames reports_wsgi.ini Commit: a3668355961e3988158a8bdb1bbe0f898d475967 https://github.com/galaxyproject/galaxy/commit/a3668355961e3988158a8bdb1bbe… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M run_reports.sh Log Message: ----------- Changed reports_wsgi.ini to reports.ini Commit: 9fceddf8a2f62df2774f269755398ce7d9f203b3 https://github.com/galaxyproject/galaxy/commit/9fceddf8a2f62df2774f26975539… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M scripts/sync_reports_config.py Log Message: ----------- Changed reports_wsgi.ini to reports.ini Commit: ca3e3760ccd92e3162a5740e713a7b3daf4c4e03 https://github.com/galaxyproject/galaxy/commit/ca3e3760ccd92e3162a5740e713a… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-27 (Fri, 27 Nov 2015) Changed paths: M .gitignore Log Message: ----------- Changed reports_wsgi.ini to reports.ini Commit: 7b85684683b3a6ee07ec024f943bada03f51195b https://github.com/galaxyproject/galaxy/commit/7b85684683b3a6ee07ec024f943b… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-29 (Sun, 29 Nov 2015) Changed paths: M run_reports.sh Log Message: ----------- Updated run_reports.sh Updated run_reports.sh to reflect new changes. Commit: 8971badb10aa216fab3ce7318ec28389e0ea79b9 https://github.com/galaxyproject/galaxy/commit/8971badb10aa216fab3ce7318ec2… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M .gitignore Log Message: ----------- Updated gitignore Commit: 9e353028d5ad5ef6a0ba7889f5f5e8b975261811 https://github.com/galaxyproject/galaxy/commit/9e353028d5ad5ef6a0ba7889f5f5… Author: Sourav Singh <souravsingh(a)users.noreply.github.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M run_reports.sh Log Message: ----------- Updated run_reports.sh Updated run_reports.sh to mark the latest changes. Commit: f35bd9ae02aaa814d9ab62838146be2ba4791f2b https://github.com/galaxyproject/galaxy/commit/f35bd9ae02aaa814d9ab62838146… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M .gitignore A config/reports.ini.sample R config/reports_wsgi.ini.sample M run_reports.sh M scripts/sync_reports_config.py Log Message: ----------- Merge pull request #1181 from souravsingh/rename_file Renames reports_wsgi.ini Compare: https://github.com/galaxyproject/galaxy/compare/c2f93316112c...f35bd9ae02aa

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[galaxyproject/galaxy] 6752fc: Fix interface and usage of WorkflowModule.get_runt...
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6752fcc100e0448d6fef6d27dacb8e2467de88ee https://github.com/galaxyproject/galaxy/commit/6752fcc100e0448d6fef6d27dacb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Fix interface and usage of WorkflowModule.get_runtime_inputs. Run workflow workflow form was broken for workflows with pause steps. Fixes #1015 (thanks @afgane). Commit: c2f93316112ce90d0f1f7fe947ce1881cae3c773 https://github.com/galaxyproject/galaxy/commit/c2f93316112ce90d0f1f7fe947ce… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/workflow/modules.py M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1174 from jmchilton/workflow_runtime_fix Fix interface and usage of WorkflowModule.get_runtime_inputs. Compare: https://github.com/galaxyproject/galaxy/compare/dc41856812f9...c2f93316112c

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[galaxyproject/galaxy] 426140: Fixes for WorkflowContentsManager requiring app du...
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4261403fad1c5fd1346b0cfe9fd25e97459cd028 https://github.com/galaxyproject/galaxy/commit/4261403fad1c5fd1346b0cfe9fd2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-25 (Wed, 25 Nov 2015) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Fixes for WorkflowContentsManager requiring app during init. Commit: dc41856812f9064c518a8e45c4559b2f32fe9db2 https://github.com/galaxyproject/galaxy/commit/dc41856812f9064c518a8e45c455… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M lib/galaxy/web/base/controller.py M lib/galaxy/webapps/galaxy/controllers/workflow.py Log Message: ----------- Merge pull request #1173 from jmchilton/wfcfix Fixes for WorkflowContentsManager requiring app during init. Compare: https://github.com/galaxyproject/galaxy/compare/1b06e8d674ed...dc41856812f9

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[galaxyproject/galaxy] bd476c: Readd jquery.migrate to galaxy.panels template bec...
by GitHub 30 Nov '15

30 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: bd476ce146d47e12b25e4faacc6ae7eeed09fbe2 https://github.com/galaxyproject/galaxy/commit/bd476ce146d47e12b25e4faacc6a… Author: jgoecks <jgoecks(a)gwu.edu> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Readd jquery.migrate to galaxy.panels template because it is needed for farbtastic, which is used in visualizations. Commit: 1b06e8d674edd7f1a1f9397429b319670891a8bd https://github.com/galaxyproject/galaxy/commit/1b06e8d674edd7f1a1f9397429b3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-30 (Mon, 30 Nov 2015) Changed paths: M templates/webapps/galaxy/galaxy.panels.mako Log Message: ----------- Merge pull request #1126 from jgoecks/farbtastic-fix Readd jquery.migrate to galaxy.panels template because it is needed f… Compare: https://github.com/galaxyproject/galaxy/compare/f4dab5523b68...1b06e8d674ed

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[galaxyproject/galaxy] 624741: add onbeforeunload to IE
by GitHub 26 Nov '15

26 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 62474100f8f075ce519d008336060dfa952da725 https://github.com/galaxyproject/galaxy/commit/62474100f8f075ce519d00833606… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- add onbeforeunload to IE Commit: f4dab5523b687c079df68d4d2988dc830429bd93 https://github.com/galaxyproject/galaxy/commit/f4dab5523b687c079df68d4d2988… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-26 (Thu, 26 Nov 2015) Changed paths: M config/plugins/interactive_environments/common/templates/ie.mako Log Message: ----------- Merge pull request #1178 from bgruening/obbeforechange_ie Prevent GIEs from being closed without user confirmation Compare: https://github.com/galaxyproject/galaxy/compare/2a54ff08292d...f4dab5523b68

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