- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] c1fe8a: Fix inconsistency in update state handling for too...
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: c1fe8aac0a646b2bed0b3dbfbf0cd75b595f1690 https://github.com/galaxyproject/galaxy/commit/c1fe8aac0a646b2bed0b3dbfbf0c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Fix inconsistency in update state handling for tool modules Commit: eaf8f4ed5056317f19950fef5e5340217fd0e809 https://github.com/galaxyproject/galaxy/commit/eaf8f4ed5056317f19950fef5e53… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/__init__.py Log Message: ----------- Extend doc tests for parameter handling Commit: 86d2b29026fc4176070d3ef5150a4f0f0ff86829 https://github.com/galaxyproject/galaxy/commit/86d2b29026fc4176070d3ef5150a… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/workflow/modules.py Log Message: ----------- Merge pull request #1993 from guerler/revise_parameters_000 Fix inconsistency in update state handling for tool modules Compare: https://github.com/galaxyproject/galaxy/compare/0a77851b9b9d...86d2b29026fc

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[galaxyproject/galaxy] ab31bd: move text out of icon spans for library dataset vi...
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ab31bd9f4865c3544a8bb8a4be8c77d41360bbed https://github.com/galaxyproject/galaxy/commit/ab31bd9f4865c3544a8bb8a4be8c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.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/library/library-dataset-view.js Log Message: ----------- move text out of icon spans for library dataset view also re-touch the html to be better readable Commit: 0a77851b9b9dba237b529c06d7fcbe3b97ab2b47 https://github.com/galaxyproject/galaxy/commit/0a77851b9b9dba237b529c06d7fc… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-24 (Thu, 24 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/library/library-dataset-view.js M static/maps/mvc/library/library-dataset-view.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/library/library-dataset-view.js Log Message: ----------- Merge pull request #2008 from martenson/libtext-from-span libraries: move text out of icon spans for library dataset view Compare: https://github.com/galaxyproject/galaxy/compare/909a5491e505...0a77851b9b9d

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[galaxyproject/galaxy] cfd937: Repack scripts
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cfd937a46e8795c4d06deb3325e18d7439390d65 https://github.com/galaxyproject/galaxy/commit/cfd937a46e8795c4d06deb3325e1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: 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 Log Message: ----------- Repack scripts Commit: 909a5491e50521c7374ef4e939e89015afe0ddde https://github.com/galaxyproject/galaxy/commit/909a5491e50521c7374ef4e939e8… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: 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 Log Message: ----------- Merge pull request #2004 from guerler/repack_000 Repack js-scripts Compare: https://github.com/galaxyproject/galaxy/compare/3b0743fab272...909a5491e505

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[galaxyproject/galaxy] 93b747: remove deprecated user-facing lib link;
by GitHub 24 Mar '16

24 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 93b7473be87813454753c9c8e58bca297a59ca2e https://github.com/galaxyproject/galaxy/commit/93b7473be87813454753c9c8e58b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- remove deprecated user-facing lib link; remove 'published' from the menu items for shared elements Commit: 3b0743fab27220824ad14a0579b960ce79b20f0c https://github.com/galaxyproject/galaxy/commit/3b0743fab27220824ad14a0579b9… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M static/maps/layout/menu.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js Log Message: ----------- Merge pull request #1996 from martenson/remove-liblink alter 'shared data' menu Compare: https://github.com/galaxyproject/galaxy/compare/fb549c80d49c...3b0743fab272

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[galaxyproject/galaxy] b51bdd: Basepanels don't have Galaxy object, causing failu...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: b51bdd06b189baccab235def65d15a69c761ac28 https://github.com/galaxyproject/galaxy/commit/b51bdd06b189baccab235def65d1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Basepanels don't have Galaxy object, causing failures in views like published tracks, etc., when resource urls are generated incorrectly Commit: dede9459b019ceb1212f4f152b4108632f892384 https://github.com/galaxyproject/galaxy/commit/dede9459b019ceb1212f4f152b41… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M templates/base/base_panels.mako Log Message: ----------- Merge pull request #2003 from dannon/trackster_debugging [16.01] Fix shared viz (and other base_panels.mako displays) early URL generation. Compare: https://github.com/galaxyproject/galaxy/compare/21e71a9b46b9...dede9459b019

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[galaxyproject/usegalaxy-playbook] 8af4f9: Add a 32 GB destination, increase the BWA-MEM DM t...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 8af4f9b38a8b14d898700befa0856acecca8c77b https://github.com/galaxyproject/usegalaxy-playbook/commit/8af4f9b38a8b14d8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M files/galaxy/common/dynamic_rules/reserved.py M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add a 32 GB destination, increase the BWA-MEM DM to 64GB

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[galaxyproject/galaxy] 7186fb: Add page layout test cases
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7186fbba9259ff9381c9253632a0269a6359cd6b https://github.com/galaxyproject/galaxy/commit/7186fbba9259ff9381c9253632a0… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js Log Message: ----------- Add page layout test cases Commit: fb549c80d49c9c89bcb94634a0ee4cafc4a6f116 https://github.com/galaxyproject/galaxy/commit/fb549c80d49c9c89bcb94634a0ee… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: A test/qunit/tests/page_tests.html A test/qunit/tests/page_tests.js Log Message: ----------- Merge pull request #1991 from guerler/fix_panel_003 Add page layout test cases Compare: https://github.com/galaxyproject/galaxy/compare/033241c99f8b...fb549c80d49c

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[galaxyproject/usegalaxy-playbook] c3d761: Mutable configs from Test
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: c3d761d62cd9a544c7f17bd80c3dcadfd4bce856 https://github.com/galaxyproject/usegalaxy-playbook/commit/c3d761d62cd9a544… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Mutable configs from Test

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[galaxyproject/usegalaxy-playbook] d7e78c: Update Jupyter image, admin users
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: d7e78ce06b34857da60d6eaa1820d9ba5e75fbcd https://github.com/galaxyproject/usegalaxy-playbook/commit/d7e78ce06b34857d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M production/group_vars/galaxyservers.yml M production/secret_vars/galaxyservers.yml M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M stage/group_vars/galaxyservers.yml Log Message: ----------- Update Jupyter image, admin users

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[galaxyproject/galaxy] 62b5f2: Remove unnecessary encoding in remote_files. This...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 62b5f207566eb9666df58f1ab107d3e7b1f0c736 https://github.com/galaxyproject/galaxy/commit/62b5f207566eb9666df58f1ab107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Remove unnecessary encoding in remote_files. This allows paths and filenames like Ăfile.txt Commit: 0c225bec2e9af0c941ccc943d9ad010f2893a6e0 https://github.com/galaxyproject/galaxy/commit/0c225bec2e9af0c941ccc943d9ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Update library_info.mako escaping. This allows use of non-ascii characters like 'This is Ă data library' Commit: 4ef186812f1d3f16b36080654ee043065237d0c5 https://github.com/galaxyproject/galaxy/commit/4ef186812f1d3f16b36080654ee0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode user_login as utf8 prior to directory manipulation. Commit: e3e49a477d96ec5fc4623646e7ea240090f80ae2 https://github.com/galaxyproject/galaxy/commit/e3e49a477d96ec5fc4623646e7ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- extreme casting to 1) make this code actually work with python 2, and 3) work should the web framework ever be functional in python3 Commit: 79d16f71f9064c1f35a0bf4c7de1191872398428 https://github.com/galaxyproject/galaxy/commit/79d16f71f9064c1f35a0bf4c7de1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map 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/masthead.js M static/scripts/layout/page.js Log Message: ----------- Fix scratchbook Commit: 8e41fda58a6b8def4f261121269c321e5dd8ff34 https://github.com/galaxyproject/galaxy/commit/8e41fda58a6b8def4f261121269c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map 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/masthead.js M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1984 from guerler/fix_scratchbook_000 [16.01] Fix scratchbook Commit: 21e71a9b46b9f4cd90b8fe5023981460775e4b59 https://github.com/galaxyproject/galaxy/commit/21e71a9b46b9f4cd90b8fe502398… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Merge pull request #1905 from dannon/library_errors [16.01] Encoding in libraries Commit: 033241c99f8bb80e4ecac2504a4bdc1f3a4dd657 https://github.com/galaxyproject/galaxy/commit/033241c99f8bb80e4ecac2504a4b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M lib/galaxy/webapps/galaxy/api/remote_files.py M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/masthead.js M static/scripts/layout/page.js M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Merge 16.01, rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/c171fd168d69...033241c99f8b

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[galaxyproject/galaxy] 62b5f2: Remove unnecessary encoding in remote_files. This...
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 62b5f207566eb9666df58f1ab107d3e7b1f0c736 https://github.com/galaxyproject/galaxy/commit/62b5f207566eb9666df58f1ab107… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Remove unnecessary encoding in remote_files. This allows paths and filenames like Ăfile.txt Commit: 0c225bec2e9af0c941ccc943d9ad010f2893a6e0 https://github.com/galaxyproject/galaxy/commit/0c225bec2e9af0c941ccc943d9ad… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Update library_info.mako escaping. This allows use of non-ascii characters like 'This is Ă data library' Commit: 4ef186812f1d3f16b36080654ee043065237d0c5 https://github.com/galaxyproject/galaxy/commit/4ef186812f1d3f16b36080654ee0… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Encode user_login as utf8 prior to directory manipulation. Commit: e3e49a477d96ec5fc4623646e7ea240090f80ae2 https://github.com/galaxyproject/galaxy/commit/e3e49a477d96ec5fc4623646e7ea… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- extreme casting to 1) make this code actually work with python 2, and 3) work should the web framework ever be functional in python3 Commit: 21e71a9b46b9f4cd90b8fe5023981460775e4b59 https://github.com/galaxyproject/galaxy/commit/21e71a9b46b9f4cd90b8fe502398… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py M templates/webapps/galaxy/library/common/library_info.mako Log Message: ----------- Merge pull request #1905 from dannon/library_errors [16.01] Encoding in libraries Compare: https://github.com/galaxyproject/galaxy/compare/8e41fda58a6b...21e71a9b46b9

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[galaxyproject/galaxy] 946458: Fix booleans
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 946458b8928be8d9ea901d280c4ec5ce36926ea1 https://github.com/galaxyproject/galaxy/commit/946458b8928be8d9ea901d280c4e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Fix booleans Commit: c171fd168d69bbc1e703f89ac94c4145d3d2a883 https://github.com/galaxyproject/galaxy/commit/c171fd168d69bbc1e703f89ac94c… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Merge pull request #1990 from guerler/fix_boolean_000 Fix booleans in workflow editor Compare: https://github.com/galaxyproject/galaxy/compare/d10ee6f6c427...c171fd168d69

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[galaxyproject/galaxy] 79d16f: Fix scratchbook
by GitHub 23 Mar '16

23 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 79d16f71f9064c1f35a0bf4c7de1191872398428 https://github.com/galaxyproject/galaxy/commit/79d16f71f9064c1f35a0bf4c7de1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map 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/masthead.js M static/scripts/layout/page.js Log Message: ----------- Fix scratchbook Commit: 8e41fda58a6b8def4f261121269c321e5dd8ff34 https://github.com/galaxyproject/galaxy/commit/8e41fda58a6b8def4f261121269c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-23 (Wed, 23 Mar 2016) Changed paths: M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/page.js M static/maps/layout/masthead.js.map M static/maps/layout/page.js.map 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/masthead.js M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1984 from guerler/fix_scratchbook_000 [16.01] Fix scratchbook Compare: https://github.com/galaxyproject/galaxy/compare/cf16b1d692d0...8e41fda58a6b

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[galaxyproject/galaxy] 133f77: Fix 'Resend verification' link in inactive user me...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 133f77413e9fb933ec1964d279408c1fb8846db4 https://github.com/galaxyproject/galaxy/commit/133f77413e9fb933ec1964d27940… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/page.js Log Message: ----------- Fix 'Resend verification' link in inactive user message box which would display as [Object object] Commit: fef166545c36df5c7ba73924c7b0ea4e1d44ec82 https://github.com/galaxyproject/galaxy/commit/fef166545c36df5c7ba73924c7b0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Layout: Fix optional panel rendering and associated inline css Commit: dd476fc42c57b5e17d8e1e342d7a597b986b6b3e https://github.com/galaxyproject/galaxy/commit/dd476fc42c57b5e17d8e1e342d7a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/page.js Log Message: ----------- Merge pull request #1978 from carlfeberhard/release_16.01 [16.01] Fixes to page.js Commit: 9eb1db82ca4bbae598d0070de8da78172ca90fa9 https://github.com/galaxyproject/galaxy/commit/9eb1db82ca4bbae598d0070de8da… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Do not convert spaces to tabs when importing datasets into a library. Reported (with fix provided) by Fabien Mareuil in http://dev.list.galaxyproject.org/automatic-adding-of-a-tab-in-a-fastq-head… Commit: cf16b1d692d0e96f3d0aa4d2cf0f9f52c8dd7bb3 https://github.com/galaxyproject/galaxy/commit/cf16b1d692d0e96f3d0aa4d2cf0f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1985 from nsoranzo/release_16.01_lda_fixes [16.01] Do not convert spaces to tabs when importing datasets into a library. Commit: d10ee6f6c42744fdd4db2981093c1411bd1be6db https://github.com/galaxyproject/galaxy/commit/d10ee6f6c42744fdd4db2981093c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M lib/galaxy/webapps/galaxy/api/lda_datasets.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge branch 'release_16.01' into dev Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js static/scripts/bundled/libs.bundled.js.map Compare: https://github.com/galaxyproject/galaxy/compare/2bbae2bb1d11...d10ee6f6c427

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[galaxyproject/galaxy] 9eb1db: Do not convert spaces to tabs when importing datas...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 9eb1db82ca4bbae598d0070de8da78172ca90fa9 https://github.com/galaxyproject/galaxy/commit/9eb1db82ca4bbae598d0070de8da… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Do not convert spaces to tabs when importing datasets into a library. Reported (with fix provided) by Fabien Mareuil in http://dev.list.galaxyproject.org/automatic-adding-of-a-tab-in-a-fastq-head… Commit: cf16b1d692d0e96f3d0aa4d2cf0f9f52c8dd7bb3 https://github.com/galaxyproject/galaxy/commit/cf16b1d692d0e96f3d0aa4d2cf0f… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/lda_datasets.py Log Message: ----------- Merge pull request #1985 from nsoranzo/release_16.01_lda_fixes [16.01] Do not convert spaces to tabs when importing datasets into a library. Compare: https://github.com/galaxyproject/galaxy/compare/dd476fc42c57...cf16b1d692d0

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[galaxyproject/galaxy] 55e8ef: Optimize adding datasets to large histories.
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 55e8ef6e1dfc2cb0721956a7801bc6e2e523ba02 https://github.com/galaxyproject/galaxy/commit/55e8ef6e1dfc2cb0721956a7801b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Optimize adding datasets to large histories. Commit: 2bbae2bb1d11c8f9e9e9d398df9b707657d28df0 https://github.com/galaxyproject/galaxy/commit/2bbae2bb1d11c8f9e9e9d398df9b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Merge pull request #1983 from jmchilton/history_append_opt Optimize adding datasets to large histories. Compare: https://github.com/galaxyproject/galaxy/compare/be78aac509bc...2bbae2bb1d11

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[galaxyproject/usegalaxy-playbook] 2eaf31: Add labels and move gemini.
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 2eaf317b3885999221b39b606004ae92478f5096 https://github.com/galaxyproject/usegalaxy-playbook/commit/2eaf317b38859992… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- Add labels and move gemini. Commit: 73c7f2e96577d664e299bf1cefbbca88581302a4 https://github.com/galaxyproject/usegalaxy-playbook/commit/73c7f2e96577d664… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml Log Message: ----------- Merge pull request #18 from davebx/clean_gemini Add labels and move gemini. Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/e9dcdbb7df55...…

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[galaxyproject/usegalaxy-playbook] 7833ec: remove slide from Main and update submodule
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7833ec74dba026b003fad88e716f5bda087a8ed6 https://github.com/galaxyproject/usegalaxy-playbook/commit/7833ec74dba026b0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M stage/files/interactive_environments/plugins/.ansible_ie_role_current_version M stage/files/interactive_environments/proxy/.ansible_ie_role_current_version M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- remove slide from Main and update submodule Commit: e9dcdbb7df55aed387db294612c82e4e95f14e6e https://github.com/galaxyproject/usegalaxy-playbook/commit/e9dcdbb7df55aed3… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_data_manager_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_conf.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M stage/group_vars/all.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Merge branch 'master' of https://github.com/galaxyproject/usegalaxy-playbook Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/9ad17375108f...…

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[galaxyproject/galaxy] 3a1c84: Remove duplicate help target
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3a1c84690239fd7a23393f0ba2e714ab8c659557 https://github.com/galaxyproject/galaxy/commit/3a1c84690239fd7a23393f0ba2e7… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M Makefile Log Message: ----------- Remove duplicate help target And reformat for using existing help-text helper Fixes #1979 Commit: 9a6d3962307f345da34f338f42eebf570562cd63 https://github.com/galaxyproject/galaxy/commit/9a6d3962307f345da34f338f42ee… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M Makefile Log Message: ----------- Fix docs Makefile target. Commit: 9d8957d121108549c1448a959aaf1061091a0bec https://github.com/galaxyproject/galaxy/commit/9d8957d121108549c1448a959aaf… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M Makefile Log Message: ----------- Document a couple other targets Commit: be78aac509bc3a84743b418544702bfca6b50eda https://github.com/galaxyproject/galaxy/commit/be78aac509bc3a84743b41854470… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M Makefile Log Message: ----------- Merge pull request #1980 from erasche/fix-1979 Remove duplicate help target Compare: https://github.com/galaxyproject/galaxy/compare/0dc57b08e851...be78aac509bc

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[galaxyproject/galaxy] 133f77: Fix 'Resend verification' link in inactive user me...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 133f77413e9fb933ec1964d279408c1fb8846db4 https://github.com/galaxyproject/galaxy/commit/133f77413e9fb933ec1964d27940… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/page.js Log Message: ----------- Fix 'Resend verification' link in inactive user message box which would display as [Object object] Commit: fef166545c36df5c7ba73924c7b0ea4e1d44ec82 https://github.com/galaxyproject/galaxy/commit/fef166545c36df5c7ba73924c7b0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js A lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_parameter_modules.py R lib/galaxy/model/migrate/versions/0131_subworkflow_and_input_paramter_modules.py M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Layout: Fix optional panel rendering and associated inline css Commit: dd476fc42c57b5e17d8e1e342d7a597b986b6b3e https://github.com/galaxyproject/galaxy/commit/dd476fc42c57b5e17d8e1e342d7a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map 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/page.js Log Message: ----------- Merge pull request #1978 from carlfeberhard/release_16.01 [16.01] Fixes to page.js Compare: https://github.com/galaxyproject/galaxy/compare/fa1414759e60...dd476fc42c57

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[galaxyproject/galaxy] 975937: Fix docker tool execution for #1688.
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 975937ec9d18287fe89a7ee9eda0952e22284ac7 https://github.com/galaxyproject/galaxy/commit/975937ec9d18287fe89a7ee9eda0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Fix docker tool execution for #1688. Thanks for @kellrott for the bug report. \#minor Commit: 0dc57b08e851544cfd1f9e4cd94de9971db2b24d https://github.com/galaxyproject/galaxy/commit/0dc57b08e851544cfd1f9e4cd94d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/containers.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #1974 from jmchilton/docker_fix Fix docker tool execution for #1688. Compare: https://github.com/galaxyproject/galaxy/compare/67b7294a7278...0dc57b08e851

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[galaxyproject/galaxy] 128a91: Checks for api_key before checking for header from...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 128a9112bb1635c1c49ac7dc1a99b531933ea659 https://github.com/galaxyproject/galaxy/commit/128a9112bb1635c1c49ac7dc1a99… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Checks for api_key before checking for header from SSO. Also fixes the NoneType issue discovered in #972. Commit: 4e12c5e782249c3aea1ddbdd5bd2f363111e78b6 https://github.com/galaxyproject/galaxy/commit/4e12c5e782249c3aea1ddbdd5bd2… Author: MatthewRalston <mrals89(a)gmail.com> Date: 2016-02-25 (Thu, 25 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Fixes NoneType problem in a simpler way. Thanks @nsoranzo. Commit: 6473057f3b63ce615727800babbaf439ed66bb3f https://github.com/galaxyproject/galaxy/commit/6473057f3b63ce615727800babba… Author: Matt Ralston <mrals89(a)gmail.com> Date: 2016-02-26 (Fri, 26 Feb 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Adds whitespace Commit: a2114fdd0e234a3253cec79a02e30899ca081359 https://github.com/galaxyproject/galaxy/commit/a2114fdd0e234a3253cec79a02e3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/remoteuser.py Log Message: ----------- Merge pull request #1801 from MatthewRalston/api_key_patch [15.10] Checks for api_key before checking for header from SSO. Compare: https://github.com/galaxyproject/galaxy/compare/9cff686d6d94...a2114fdd0e23

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[galaxyproject/usegalaxy-playbook] 9ad173: Increase BMW-MEM indexer to 16GB of memory and run...
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9ad17375108fc081cc6f063c8d768a69ec56295c https://github.com/galaxyproject/usegalaxy-playbook/commit/9ad17375108fc081… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Increase BMW-MEM indexer to 16GB of memory and run it with the datamanager server as its handler.

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[galaxyproject/galaxy] eee044: Work toward automating deployment.
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: eee044aa707f9fa6d4c800b4d655fd01b2e08e84 https://github.com/galaxyproject/galaxy/commit/eee044aa707f9fa6d4c800b4d655… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M Makefile M doc/source/releases/index.rst M scripts/bootstrap_history.py Log Message: ----------- Work toward automating deployment. Create new makefile targets for release management. - ``release-create-issue``: Automates creating a release checklist - https://github.com/jmchilton/galaxy/issues/41) Check list contains actual tailored ``make`` commands and links (for PRs and issues). - ``release-check-metadata``: Checks milestone PRs for required metadata needed for generating bootstrapped release notes. ` ``release-bootstrap-history``: Bootstrap release notes from PRs and metadata. - ``release-check-blocking-prs``: Check for PRs blocking release, should happen before branching release and before tagging release. - ``release-check-blocking-issues``: Check for Issues blocking release, should happen before tagging release. (Only allowed issue is the release creation issue.) The issue created with ``release-create-issue`` documents how and when to execute subsequent ``make`` targets (including the target to create the issue for the next release). This PR contains a bunch of other enhancements to the bootstrap_history.py script to enable these targets and renames ``create_release_rc`` Makefile target so all release related targets start with the prefix ``release-``. Conflicts: Makefile Commit: 67b7294a7278f262f0e2238b0094cef5fc835771 https://github.com/galaxyproject/galaxy/commit/67b7294a7278f262f0e2238b0094… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M Makefile M doc/source/releases/index.rst M scripts/bootstrap_history.py Log Message: ----------- Merge pull request #1613 from jmchilton/release_process Work toward automating release management. Compare: https://github.com/galaxyproject/galaxy/compare/4bf8adbb6462...67b7294a7278

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[galaxyproject/galaxy] 583461: Fix dom duplication
by GitHub 22 Mar '16

22 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 58346169dfbe89f845a3f2317bde514c3e65f79f https://github.com/galaxyproject/galaxy/commit/58346169dfbe89f845a3f2317bde… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Fix dom duplication Commit: fa1414759e604073bc45fe3f2b15dc9f21c72c4c https://github.com/galaxyproject/galaxy/commit/fa1414759e604073bc45fe3f2b15… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge pull request #1976 from guerler/fix_ui_000 [16.01] Fix dom duplication Commit: 4bf8adbb6462456a201a6f69862e0d3fdb1da222 https://github.com/galaxyproject/galaxy/commit/4bf8adbb6462456a201a6f69862e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-22 (Tue, 22 Mar 2016) Changed paths: M client/galaxy/scripts/layout/page.js M static/maps/layout/page.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/page.js Log Message: ----------- Merge, rebuild. Compare: https://github.com/galaxyproject/galaxy/compare/45c17318889d...4bf8adbb6462

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