- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 05ed24: Fix the bad merge :(
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 05ed245353331489ee443ac483b1569dab38f500 https://github.com/galaxyproject/galaxy/commit/05ed245353331489ee443ac483b1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_review_grids.py Log Message: ----------- Fix the bad merge :(

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[galaxyproject/galaxy] 05f3da: Fix macro bug with empty CDATA being None instead ...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 05f3da308d6a58dc8528f317fa6ea4ffa1fb7610 https://github.com/galaxyproject/galaxy/commit/05f3da308d6a58dc8528f317fa6e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Fix macro bug with empty CDATA being None instead of ''. Fixes galaxyproject/planemo#362 thanks for the report @erasche. Test using the following command: ``` nosetests test/unit/tools/test_tool_loader.py ``` Commit: eb16ba3743a7e42cc9ad43f0d7a3eb926ba60cd8 https://github.com/galaxyproject/galaxy/commit/eb16ba3743a7e42cc9ad43f0d7a3… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/util/xml_macros.py M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge pull request #1122 from jmchilton/empty_cdata_macro [15.10] Fix macro bug with empty CDATA being None instead of ''. Commit: 0fdca7d40a2297ec29ea9df383578626141fcfa7 https://github.com/galaxyproject/galaxy/commit/0fdca7d40a2297ec29ea9df38357… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name). Commit: f61ec1c3c01b51fe3449a583e1966cc3dff099f2 https://github.com/galaxyproject/galaxy/commit/f61ec1c3c01b51fe3449a583e196… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/util/xml_macros.py M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js M test/unit/tools/test_tool_loader.py Log Message: ----------- Merge and rebuild client Compare: https://github.com/galaxyproject/galaxy/compare/96b17bd8560f...f61ec1c3c01b

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[galaxyproject/galaxy] 0fdca7: A large assortment of escaping fixes to primarily ...
by GitHub 20 Nov '15

20 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: 0fdca7d40a2297ec29ea9df383578626141fcfa7 https://github.com/galaxyproject/galaxy/commit/0fdca7d40a2297ec29ea9df38357… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/history/copy-dialog.js M client/galaxy/scripts/mvc/history/history-panel.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-li.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/toolshed/scripts/mvc/groups/group-detail-view.js M client/toolshed/scripts/mvc/groups/group-listrow-view.js M lib/galaxy/webapps/galaxy/controllers/admin.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/external_service.py M lib/galaxy/webapps/galaxy/controllers/forms.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/library.py M lib/galaxy/webapps/galaxy/controllers/library_admin.py M lib/galaxy/webapps/galaxy/controllers/request_type.py M lib/galaxy/webapps/galaxy/controllers/requests_admin.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/reports/controllers/sample_tracking.py M lib/galaxy/webapps/reports/controllers/workflows.py M lib/tool_shed/grids/admin_grids.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/grids/repository_review_grids.py M static/maps/mvc/history/copy-dialog.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/jquery.dynatree.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/history/copy-dialog.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-li.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- A large assortment of escaping fixes to primarily grids and javascript templating, and one bad-data-ingress fix (copy history name).

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[galaxyproject/galaxy] 704144: Don't let $input hang cheetah evaluation...
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 704144c16936e6ddedee9d509ee4361f50f152f2 https://github.com/galaxyproject/galaxy/commit/704144c16936e6ddedee9d509ee4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/tools/evaluation.py Log Message: ----------- Don't let $input hang cheetah evaluation... If $input is undefined. The Python input command was being used and causing Galaxy to hang during evaluation. Commit: 0ff8a21891f7780dd30f81047cb5f8112c924b4a https://github.com/galaxyproject/galaxy/commit/0ff8a21891f7780dd30f81047cb5… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/tools/evaluation.py A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add example tools demonstrating cheetah problem (unbound variable). Refine default override of input to raise an exception instead of just throwing in a dummy string. Commit: 7dedb3ff18f06b123ac9d64ac1d9b42948ba903c https://github.com/galaxyproject/galaxy/commit/7dedb3ff18f06b123ac9d64ac1d9… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: A test/functional/tools/cheetah_problem_syntax_error.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add another cheetah syntax error example... ... ensure the test framework run the tool, detects that there is an error, and handles things appropriately. Commit: 96b17bd8560f938ee9d3244b6cf5b198864c44ce https://github.com/galaxyproject/galaxy/commit/96b17bd8560f938ee9d3244b6cf5… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/tools/evaluation.py A test/functional/tools/cheetah_problem_syntax_error.xml A test/functional/tools/cheetah_problem_unbound_var.xml A test/functional/tools/cheetah_problem_unbound_var_input.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1117 from jmchilton/input_hang Don't let $input hang cheetah evaluation... Compare: https://github.com/galaxyproject/galaxy/compare/81f842743d0c...96b17bd8560f

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[galaxyproject/galaxy] af36ca: add BAM iobio visualisation as Interactive Environ...
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: af36ca6d9467932036d19a448ca4c74affffae9a https://github.com/galaxyproject/galaxy/commit/af36ca6d9467932036d19a448ca4… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- add BAM iobio visualisation as Interactive Environment Commit: 5188b4179063b3cc57c5c983d48a5fb62387d2b3 https://github.com/galaxyproject/galaxy/commit/5188b4179063b3cc57c5c983d48a… Author: Bjoern Gruening <bjoern.gruening(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- make travis happy Commit: 81f842743d0c42522f7f80b603eccbc78d697a3c https://github.com/galaxyproject/galaxy/commit/81f842743d0c42522f7f80b603ec… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.ini.sample A config/plugins/interactive_environments/bam_iobio/config/bam_iobio.xml A config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js A config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako M config/plugins/interactive_environments/common/templates/ie.mako M config/plugins/interactive_environments/ipython/config/ipython.ini.sample M config/plugins/interactive_environments/ipython/static/js/ipython.js M config/plugins/interactive_environments/rstudio/static/js/rstudio.js M lib/galaxy/web/base/interactive_environments.py Log Message: ----------- Merge pull request #1131 from bgruening/IE_iobio Add BAM iobio visualisation as Interactive Environment Compare: https://github.com/galaxyproject/galaxy/compare/5191c2136a91...81f842743d0c

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[galaxyproject/infrastructure-playbook] 1654f5: install proper legacy node
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 1654f593b3914429f1a48a618f64f641ec10a94c https://github.com/galaxyproject/infrastructure-playbook/commit/1654f593b39… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M galaxyenv/host_vars/leeroy.galaxyproject.org.yml Log Message: ----------- install proper legacy node

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[galaxyproject/infrastructure-playbook] 3e0e46: Update common roles
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 3e0e465b377ee162fb229aaed31289dd54a9ac60 https://github.com/galaxyproject/infrastructure-playbook/commit/3e0e465b377… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M common_roles Log Message: ----------- Update common roles Commit: 93e257eddb50eddac81d4ed157e56cdd36e30d63 https://github.com/galaxyproject/infrastructure-playbook/commit/93e257eddb5… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M galaxyenv/playbook.yml M taccenv/playbook.yml Log Message: ----------- Handle renamed files role Commit: d646f4f68d73a71512ce193459ad92e062b5a9f1 https://github.com/galaxyproject/infrastructure-playbook/commit/d646f4f68d7… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A galaxyenv/files/orval/rsyncd.xml M galaxyenv/host_vars/orval.galaxyproject.org.yml Log Message: ----------- Make orval serve packages over rsync Compare: https://github.com/galaxyproject/infrastructure-playbook/compare/a03d2b5c15…

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[galaxyproject/infrastructure-playbook] a03d2b: jenkins is dead, long live jenkins
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: a03d2b5c15aa7c645ef2a8d2fce464567b53a56f https://github.com/galaxyproject/infrastructure-playbook/commit/a03d2b5c15a… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: A galaxyenv/host_vars/leeroy.galaxyproject.org.yml R galaxyenv/host_vars/n2.galaxyproject.org.yml M galaxyenv/host_vars/westvleteren.galaxyproject.org.yml M galaxyenv/inventory M galaxyenv/secret_group_vars/all.yml A galaxyenv/secret_host_vars/leeroy.galaxyproject.org.yml R galaxyenv/secret_host_vars/n2.galaxyproject.org.yml M galaxyenv/secret_host_vars/orval.galaxyproject.org.yml M galaxyenv/secret_host_vars/westvleteren.galaxyproject.org.yml M roles/linuxbrew/tasks/main.yml Log Message: ----------- jenkins is dead, long live jenkins

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[galaxyproject/galaxy] a3fee0: Style: fix state-success-bg change that was not re...
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: a3fee086c6dee9a688ffb7da13f71c1210cb76da https://github.com/galaxyproject/galaxy/commit/a3fee086c6dee9a688ffb7da13f7… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- Style: fix state-success-bg change that was not reverted during 5fd4daf Commit: 5191c2136a9131005533faff4b0c1267f1ce35c1 https://github.com/galaxyproject/galaxy/commit/5191c2136a9131005533faff4b0c… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M client/galaxy/style/less/galaxy_bootstrap/variables.less Log Message: ----------- Merge pull request #1129 from carlfeberhard/fix.styles Style: fix state-success-bg change that was not reverted during 5fd4daf Compare: https://github.com/galaxyproject/galaxy/compare/d2bab13fa92a...5191c2136a91

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[galaxyproject/galaxy] b25b8c: Revise and fix waiting for tool tests.
by GitHub 19 Nov '15

19 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b25b8c3f243e87a196a6cb0fa23328ee7c7e26f7 https://github.com/galaxyproject/galaxy/commit/b25b8c3f243e87a196a6cb0fa233… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-18 (Wed, 18 Nov 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Revise and fix waiting for tool tests. - maxseconds on test tag stopped being respected at some point, fix that. - maxseconds on test tag stopped being parsed at some later point, fix that. - Revise default behavior so it can be overridden with yet another testing environment variable GALAXY_TEST_DEFAULT_WAIT. - Add test case to ensure there is no future regression of these behaviors. Commit: d2bab13fa92a87a3c4959d782ba0bf061ecf07db https://github.com/galaxyproject/galaxy/commit/d2bab13fa92a87a3c4959d782ba0… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-19 (Thu, 19 Nov 2015) Changed paths: M lib/galaxy/tools/parser/xml.py M lib/galaxy/tools/test.py M test/base/twilltestcase.py A test/functional/tools/maxseconds.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #1119 from jmchilton/maxseconds Revise and fix waiting for tool tests. Compare: https://github.com/galaxyproject/galaxy/compare/7ab070e9df6e...d2bab13fa92a

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