- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy]
by GitHub 30 Nov '15

30 Nov '15

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

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[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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