- galaxy-commits - lists.galaxyproject.org

[galaxyproject/infrastructure-playbook] 41f8d6: install postgresql-9.4 on n2
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/martenson-patch-1 Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 41f8d6cc7e261b9f200ccc8e0efb57e41d8e846f https://github.com/galaxyproject/infrastructure-playbook/commit/41f8d6cc7e2… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- install postgresql-9.4 on n2

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[galaxyproject/galaxy] 85480e: Fix Galaxy.user to be available when not using 1 r...
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 85480e72bfa62306d19ac03ff60b4406f01146e0 https://github.com/galaxyproject/galaxy/commit/85480e72bfa62306d19ac03ff60b… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Fix Galaxy.user to be available when not using 1 require Commit: 08668104e5aa9c564dba561bab403439a65cd0fd https://github.com/galaxyproject/galaxy/commit/08668104e5aa9c564dba561bab40… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M templates/webapps/galaxy/galaxy.masthead.mako Log Message: ----------- Merge pull request #728 from carlfeberhard/fix.galaxy-user Fix Galaxy.user to be available when not using 1 require Compare: https://github.com/galaxyproject/galaxy/compare/ba2505792259...08668104e5aa

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[galaxyproject/galaxy] 8f1d3c: Dedupe one of the worse offenders
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8f1d3cac8d4506053d252687194962b7ee81538d https://github.com/galaxyproject/galaxy/commit/8f1d3cac8d4506053d2526871949… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Dedupe one of the worse offenders Commit: 5415e295ac4bf00e9ed9a903ae908c06f57ee0d4 https://github.com/galaxyproject/galaxy/commit/5415e295ac4bf00e9ed9a903ae90… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py Log Message: ----------- Refactor sleeper duplications Commit: 673c1cdbca1ce3bf9ce561c3041d5fa33a8275e8 https://github.com/galaxyproject/galaxy/commit/673c1cdbca1ce3bf9ce561c3041d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Refactor identical role queries into a single function Commit: a71ac4ee3144e1463064730a297627c9797382f6 https://github.com/galaxyproject/galaxy/commit/a71ac4ee3144e1463064730a2976… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/util.py Log Message: ----------- Refactor copy-pasted function into separate module Commit: 7cd241f0d9dfb0d4b20bd1c3902a1405258f682d https://github.com/galaxyproject/galaxy/commit/7cd241f0d9dfb0d4b20bd1c3902a… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/security/__init__.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py A lib/galaxy/webapps/util.py Log Message: ----------- Merge branch 'big-dedup' into deduplication Commit: 1a2413f8793dee35ae237003f743ac80df17ef74 https://github.com/galaxyproject/galaxy/commit/1a2413f8793dee35ae237003f743… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/reports/controllers/jobs.py Log Message: ----------- Refactor duplicate calculation code in reports Commit: 6dd4b2b11f14882e3d129261de950e6b61e5bbc0 https://github.com/galaxyproject/galaxy/commit/6dd4b2b11f14882e3d129261de95… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/repository.py Log Message: ----------- Correct copy-pasted typo Commit: 28143581d9270dc880433dd80687a47076d9ccd1 https://github.com/galaxyproject/galaxy/commit/28143581d9270dc880433dd80687… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/tool_shed/buildapp.py Log Message: ----------- Make flake8 happy Commit: 1aa7ef12ec88e469f5e635b9c28cd4f9055ceb33 https://github.com/galaxyproject/galaxy/commit/1aa7ef12ec88e469f5e635b9c28c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Refactor into a single method and flake Commit: a437083d429f605485745ce82b19c4825c57c161 https://github.com/galaxyproject/galaxy/commit/a437083d429f605485745ce82b19… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/topsort.py Log Message: ----------- refactor completely duplicated numpreds/successor processing Commit: 15edae24c8e3fae058aa7c7d017d47467febb5ff https://github.com/galaxyproject/galaxy/commit/15edae24c8e3fae058aa7c7d017d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-03 (Thu, 03 Sep 2015) Changed paths: M lib/galaxy/util/topsort.py Log Message: ----------- Fix formatting error Commit: 5fc366f7f7fa1231b2c1c643f2e3ff4bae2d26de https://github.com/galaxyproject/galaxy/commit/5fc366f7f7fa1231b2c1c643f2e3… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/security/__init__.py Log Message: ----------- Correct typo'd _get_roles function Commit: 060fdffda8b2d4b0c7aad3e460248b3793fdb69d https://github.com/galaxyproject/galaxy/commit/060fdffda8b2d4b0c7aad3e46024… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-04 (Fri, 04 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Correct import for @nsoranzo Commit: d3fa5066ca6e9ee23a25427050d3573f522bb1e0 https://github.com/galaxyproject/galaxy/commit/d3fa5066ca6e9ee23a25427050d3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Fix wrong local import of galaxy. Commit: f2d7917cfca995ba6c8ea77e0475360b59496576 https://github.com/galaxyproject/galaxy/commit/f2d7917cfca995ba6c8ea77e0475… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Merge pull request #8 from nsoranzo/fix_for_erasche Fix wrong local import of galaxy. Commit: 1f3486cb517a54c7dd9ae4a8c9020d07745774f6 https://github.com/galaxyproject/galaxy/commit/1f3486cb517a54c7dd9ae4a8c902… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py Log Message: ----------- Initialized variables Commit: d95b1cd37a564f6f72e6bfc453b09ed010c3e19a https://github.com/galaxyproject/galaxy/commit/d95b1cd37a564f6f72e6bfc453b0… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2015-09-07 (Mon, 07 Sep 2015) Changed paths: M lib/galaxy/webapps/util.py Log Message: ----------- Merge branch 'deduplication' of github.com:erasche/galaxy into deduplication Commit: 17d8e15e4ee696610799a46abdf3d0379e9d23d5 https://github.com/galaxyproject/galaxy/commit/17d8e15e4ee696610799a46abdf3… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/security/__init__.py M lib/galaxy/util/topsort.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py A lib/galaxy/webapps/util.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Merge remote-tracking branch 'erasche/deduplication' into deduplication-merge Conflicts: lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Commit: 57634f43ea4ed82bf2603df80545604d795e3896 https://github.com/galaxyproject/galaxy/commit/57634f43ea4ed82bf2603df80545… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Fix lint problems from merge. How did that happen, those pieces of code were largely unrelated. Ekkk... Commit: ba25057922594b1d2878ccf5e96dd83ffc0843a3 https://github.com/galaxyproject/galaxy/commit/ba25057922594b1d2878ccf5e96d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/jobs/deferred/__init__.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/security/__init__.py M lib/galaxy/util/topsort.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/reports/buildapp.py M lib/galaxy/webapps/reports/controllers/jobs.py M lib/galaxy/webapps/tool_shed/buildapp.py M lib/galaxy/webapps/tool_shed/controllers/repository.py A lib/galaxy/webapps/util.py M lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py M lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py Log Message: ----------- Merge pull request #694 from erasche/deduplication Deduplication PR Compare: https://github.com/galaxyproject/galaxy/compare/1ba64709e668...ba2505792259

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[galaxyproject/galaxy] 857755: Fix multi-history copy/new to set the history as c...
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 857755284db6ba2c6a773e01050222ba9748e616 https://github.com/galaxyproject/galaxy/commit/857755284db6ba2c6a773e010502… Author: Carl Eberhard <carlfeberhard(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- Fix multi-history copy/new to set the history as current Commit: 1ba64709e668f08ce757606a784aec19f7a840d1 https://github.com/galaxyproject/galaxy/commit/1ba64709e668f08ce757606a784a… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/history/history-model.js M static/maps/mvc/history/history-model.js.map M static/scripts/mvc/history/history-model.js Log Message: ----------- Merge pull request #727 from carlfeberhard/fix.multi-new Fix multi-history copy/new to set the history as current Compare: https://github.com/galaxyproject/galaxy/compare/2844d8579b5e...1ba64709e668

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[galaxyproject/galaxy] 222d78: Fix history options menu
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 222d7805e9a36b5d9b1e31377f1fb35f3405f084 https://github.com/galaxyproject/galaxy/commit/222d7805e9a36b5d9b1e31377f1f… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix history options menu Commit: 08fef5843894317b791559e7dc2aa54bb720aed3 https://github.com/galaxyproject/galaxy/commit/08fef5843894317b791559e7dc2a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Fix purge flag in history options Commit: 2844d8579b5e84c81b22a662ca4d1211f96f39d3 https://github.com/galaxyproject/galaxy/commit/2844d8579b5e84c81b22a662ca4d… Author: Aysam Guerler <aysam.guerler(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M client/galaxy/scripts/mvc/app/app-analysis.js M static/maps/mvc/app/app-analysis.js.map M static/scripts/mvc/app/app-analysis.js Log Message: ----------- Merge pull request #726 from guerler/fix_history_000 Fix history option flags Compare: https://github.com/galaxyproject/galaxy/compare/b51294efba3b...2844d8579b5e

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[galaxyproject/galaxy] 8c2ab4: Extend root controller to allow specifing a histor...
by GitHub 14 Sep '15

14 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8c2ab4180b218c3cffcf5c739ccbe4d22c52edaa https://github.com/galaxyproject/galaxy/commit/8c2ab4180b218c3cffcf5c739ccb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Extend root controller to allow specifing a history id. It currently allows hoping straight to a given workflow or tool by id, this commit extends that to allow histories as well. Simply add history_id=<history_id> to the query string. Commit: b51294efba3ba018bab6b7f5d9234196f7712adc https://github.com/galaxyproject/galaxy/commit/b51294efba3ba018bab6b7f5d923… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-14 (Mon, 14 Sep 2015) Changed paths: M lib/galaxy/webapps/galaxy/controllers/root.py Log Message: ----------- Merge pull request #725 from jmchilton/history_id_entry Extend root controller to allow specifying a history id. Compare: https://github.com/galaxyproject/galaxy/compare/51979deefbd9...b51294efba3b

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[galaxyproject/galaxy] 76ad95: Fix lint failure in toolshed/admin.
by GitHub 13 Sep '15

13 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76ad959f16e0f30a8e306056ab8042ba8512b9a9 https://github.com/galaxyproject/galaxy/commit/76ad959f16e0f30a8e306056ab80… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Fix lint failure in toolshed/admin. Commit: 51979deefbd98858987d7c93495743300845c90c https://github.com/galaxyproject/galaxy/commit/51979deefbd98858987d7c934957… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-13 (Sun, 13 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Merge pull request #722 from dannon/style_fix Fix lint failure in toolshed/admin. Compare: https://github.com/galaxyproject/galaxy/compare/fef28884fc6f...51979deefbd9

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[galaxyproject/usegalaxy-playbook] 41bc8a: Update Test Galaxy and Pulsar
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 41bc8a7d80e99b1c405a72254729a223e4a625b9 https://github.com/galaxyproject/usegalaxy-playbook/commit/41bc8a7d80e99b1c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M stage/group_vars/all.yml M stage/group_vars/pulsarservers.yml Log Message: ----------- Update Test Galaxy and Pulsar

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[galaxyproject/galaxy] 63a715: Fix Tool Shed test broken with PR #706.
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 63a715f27c5ee31de6bdd0cd4222b309b3f2ce23 https://github.com/galaxyproject/galaxy/commit/63a715f27c5ee31de6bdd0cd4222… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/tool_shed/functional/test_1140_tool_help_images.py Log Message: ----------- Fix Tool Shed test broken with PR #706. Commit: ed92a12e78dad1d7290fde30b23768b613e68232 https://github.com/galaxyproject/galaxy/commit/ed92a12e78dad1d7290fde30b237… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/workflow/modules.py Log Message: ----------- Specify the tool_id of the missing tool when raising MissingToolException. Commit: 760899f9c0ce717df4e6c789e36693973d048c7d https://github.com/galaxyproject/galaxy/commit/760899f9c0ce717df4e6c789e366… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/api/test_workflows.py Log Message: ----------- Fix MissingToolException when running "./run_tests.sh -api" without "-with_framework_test_tools". Commit: 65519718b37a0a08c802c131b92ca0335a0b7eda https://github.com/galaxyproject/galaxy/commit/65519718b37a0a08c802c131b92c… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M test/api/yaml_to_workflow.py Log Message: ----------- Fix "KeyError: name" error when running "./run_tests.sh -api". Example traceback for test/api/test_workflows.py:WorkflowsApiTestCase.test_workflow_run_dynamic_output_collections : galaxy.web.framework.decorators: ERROR: Uncaught exception in exposed API method: Traceback (most recent call last): File "/opt/galaxy/lib/galaxy/web/framework/decorators.py", line 260, in decorator rval = func( self, trans, *args, **kwargs) File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 182, in create return self.__api_import_new_workflow( trans, payload, **kwd ) File "/opt/galaxy/lib/galaxy/webapps/galaxy/api/workflows.py", line 374, in __api_import_new_workflow workflow, missing_tool_tups = self._workflow_from_dict( trans, data, **from_dict_kwds ) File "/opt/galaxy/lib/galaxy/web/base/controller.py", line 1111, in _workflow_from_dict publish=publish File "/opt/galaxy/lib/galaxy/managers/workflows.py", line 165, in build_workflow_from_dict missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) KeyError: 'name' Commit: cd456e186dc1ba6f51e3cafb0c54d6b1f1651817 https://github.com/galaxyproject/galaxy/commit/cd456e186dc1ba6f51e3cafb0c54… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M scripts/check_galaxy.py Log Message: ----------- Print to stderr when calling sys.exit(1) Commit: c01cf85d450a83c4f235ba488b84d2c7a60c4209 https://github.com/galaxyproject/galaxy/commit/c01cf85d450a83c4f235ba488b84… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M doc/source/conf.py M lib/galaxy/main.py M lib/galaxy_ext/metadata/set_metadata.py M test/base/tool_shed_util.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/functional_tests.py M test/unit/unittest_utils/utility.py Log Message: ----------- Use __file__ when adding paths to sys.path instead of os.getcwd() . Also insert additional paths in position 1 unless strictly necessary. Commit: fef28884fc6f46efb01816c9466667840947f372 https://github.com/galaxyproject/galaxy/commit/fef28884fc6f46efb01816c94666… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M cron/add_manual_builds.py M cron/build_chrom_db.py M cron/cleanup_datasets.py M doc/source/conf.py M lib/galaxy/main.py M lib/galaxy/workflow/modules.py M lib/galaxy_ext/metadata/set_metadata.py M scripts/check_galaxy.py M test/api/test_workflows.py M test/api/yaml_to_workflow.py M test/base/tool_shed_util.py M test/install_and_test_tool_shed_repositories/base/util.py M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py M test/manual/workflows_scaling.py M test/tool_shed/functional/test_1140_tool_help_images.py M test/tool_shed/functional_tests.py M test/unit/unittest_utils/utility.py Log Message: ----------- Merge pull request #720 from nsoranzo/misc_fixes Misc fixes Compare: https://github.com/galaxyproject/galaxy/compare/36809cd6f37f...fef28884fc6f

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[galaxyproject/galaxy] 819c7d: Pulsar client: Fix deepcopy() error with copying t...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 819c7dce408f35f69457cd92803c63cf3efca0c4 https://github.com/galaxyproject/galaxy/commit/819c7dce408f35f69457cd92803c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange. Commit: 36809cd6f37f65e9b571a0eb3e663419930e5871 https://github.com/galaxyproject/galaxy/commit/36809cd6f37f65e9b571a0eb3e66… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge branch 'amqp_ack' into test Compare: https://github.com/galaxyproject/galaxy/compare/91799c3891fe...36809cd6f37f

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[galaxyproject/galaxy] 819c7d: Pulsar client: Fix deepcopy() error with copying t...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 819c7dce408f35f69457cd92803c63cf3efca0c4 https://github.com/galaxyproject/galaxy/commit/819c7dce408f35f69457cd92803c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange. Commit: 88abd3451d1b8cb7161fde7559684d5378dc76fc https://github.com/galaxyproject/galaxy/commit/88abd3451d1b8cb7161fde755968… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py Log Message: ----------- Merge pull request #719 from natefoo/amqp_ack [15.07] Pulsar client: Fix deepcopy() error with copying the errback method from PulsarExchange. Compare: https://github.com/galaxyproject/galaxy/compare/358dc4071462...88abd3451d1b

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[galaxyproject/galaxy] d41c13: Fix for logging in using OpenID when the OpenID is...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: d41c137e2d6b4d9871bb25c5162745dda36e2f31 https://github.com/galaxyproject/galaxy/commit/d41c137e2d6b4d9871bb25c51627… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Fix for logging in using OpenID when the OpenID isn't associated with a user yet. (cherry picked from commit 451196e4d39800995d7b1ea1f69b177294c3c632) Commit: 358dc4071462347dacecd1f6ec125d650b261db0 https://github.com/galaxyproject/galaxy/commit/358dc4071462347dacecd1f6ec12… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Merge pull request #718 from blankenberg/openid_15.07 [15.07] Fix for logging in using OpenID when the OpenID isn't associated with a user yet. Compare: https://github.com/galaxyproject/galaxy/compare/16fb094f1a10...358dc4071462

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[galaxyproject/usegalaxy-playbook] 6a7350: Fix secret vars path for updating Galaxy on Pulsar...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6a73502f1c8ace9f721427ef6f0c24e59fe33ae3 https://github.com/galaxyproject/usegalaxy-playbook/commit/6a73502f1c8ace9f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M galaxy.yml Log Message: ----------- Fix secret vars path for updating Galaxy on Pulsar servers

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[galaxyproject/usegalaxy-playbook] 18417d: Update Test Galaxy and Pulsar, enable AMQP acknowl...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 18417dd20bf1ea56bf2e162b16ac64c545f21334 https://github.com/galaxyproject/usegalaxy-playbook/commit/18417dd20bf1ea56… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M stage/group_vars/all.yml M stage/group_vars/pulsarservers.yml M stage/host_vars/greenfield.psc.xsede.org.yml M stage/host_vars/login5.stampede.tacc.utexas.edu.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Update Test Galaxy and Pulsar, enable AMQP acknowledgements

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[galaxyproject/galaxy] e95145: With Pulsar, ensure AMQP consumers receive publish...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e951455be37a787a26678e66e607004a9b8ce954 https://github.com/galaxyproject/galaxy/commit/e951455be37a787a26678e66e607… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- With Pulsar, ensure AMQP consumers receive published messages. Commit: 5bae90156fa7998b575981ac452db21f34683085 https://github.com/galaxyproject/galaxy/commit/5bae90156fa7998b575981ac452d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/util.py Log Message: ----------- Fix a couple flake8 errors including a supposed PEP-8 violation that is actually a PEP-8-suggested acceptable option of how to handle the offending situation. =P Commit: 8778da43cb641a925c421b188aabe053be56e313 https://github.com/galaxyproject/galaxy/commit/8778da43cb641a925c421b188aab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/manager.py Log Message: ----------- Disable amqp_acknowledge by default, additional fixes from Pulsar's pickier flake8 checks. Commit: ff8e821013e59527bb2bdfacffef2a2db7e562d2 https://github.com/galaxyproject/galaxy/commit/ff8e821013e59527bb2bdfacffef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- Merge pull request #704 from natefoo/amqp_ack [15.07] With Pulsar, ensure AMQP consumers receive published messages Commit: 448ff738f35ad3f8d627257f46c681a6a4907778 https://github.com/galaxyproject/galaxy/commit/448ff738f35ad3f8d627257f46c6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- fix incorrect indentation preventing changing of name/description of TS categories Commit: 16fb094f1a101064d6f2981166b060b1ba30aa0e https://github.com/galaxyproject/galaxy/commit/16fb094f1a101064d6f2981166b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Merge pull request #717 from martenson/fix-ts-edit-category [15.07] fix incorrect indentation preventing changing of name/description Commit: 91799c3891fe60f94fc52501541326904cc96071 https://github.com/galaxyproject/galaxy/commit/91799c3891fe60f94fc525015413… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/webapps/tool_shed/controllers/admin.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- Merge branch 'release_15.07' into dev Compare: https://github.com/galaxyproject/galaxy/compare/c9ef883db64b...91799c3891fe

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[galaxyproject/galaxy] 448ff7: fix incorrect indentation preventing changing of n...
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: 448ff738f35ad3f8d627257f46c681a6a4907778 https://github.com/galaxyproject/galaxy/commit/448ff738f35ad3f8d627257f46c6… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- fix incorrect indentation preventing changing of name/description of TS categories Commit: 16fb094f1a101064d6f2981166b060b1ba30aa0e https://github.com/galaxyproject/galaxy/commit/16fb094f1a101064d6f2981166b0… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M lib/galaxy/webapps/tool_shed/controllers/admin.py Log Message: ----------- Merge pull request #717 from martenson/fix-ts-edit-category [15.07] fix incorrect indentation preventing changing of name/description Compare: https://github.com/galaxyproject/galaxy/compare/ff8e821013e5...16fb094f1a10

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[galaxyproject/infrastructure-playbook] 113caf: Install git on n2
by GitHub 11 Sep '15

11 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 113caf158f19ced6abfc95152328e8bf38db5f06 https://github.com/galaxyproject/infrastructure-playbook/commit/113caf158f1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-11 (Fri, 11 Sep 2015) Changed paths: M galaxyenv/host_vars/n2.galaxyproject.org.yml Log Message: ----------- Install git on n2

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[galaxyproject/galaxy] 451196: Fix for logging in using OpenID when the OpenID is...
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 451196e4d39800995d7b1ea1f69b177294c3c632 https://github.com/galaxyproject/galaxy/commit/451196e4d39800995d7b1ea1f69b… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Fix for logging in using OpenID when the OpenID isn't associated with a user yet. Commit: c9ef883db64bbf9e2d4f9b8bc2dea11f8e4be60d https://github.com/galaxyproject/galaxy/commit/c9ef883db64bbf9e2d4f9b8bc2de… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M templates/user/login.mako Log Message: ----------- Merge pull request #712 from blankenberg/openid_associate_fix Fix for logging in using OpenID when the OpenID isn't associated Compare: https://github.com/galaxyproject/galaxy/compare/b79555264e6f...c9ef883db64b

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[galaxyproject/galaxy]
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/revert-704-amqp_ack Home: https://github.com/galaxyproject/galaxy

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[galaxyproject/galaxy] fab314: Revert "[15.07] With Pulsar, ensure AMQP consumers...
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/revert-704-amqp_ack Home: https://github.com/galaxyproject/galaxy Commit: fab314265f7e14c0bc488b25bbff27074c0dd1be https://github.com/galaxyproject/galaxy/commit/fab314265f7e14c0bc488b25bbff… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- Revert "[15.07] With Pulsar, ensure AMQP consumers receive published messages"

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[galaxyproject/galaxy] e95145: With Pulsar, ensure AMQP consumers receive publish...
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/release_15.07 Home: https://github.com/galaxyproject/galaxy Commit: e951455be37a787a26678e66e607004a9b8ce954 https://github.com/galaxyproject/galaxy/commit/e951455be37a787a26678e66e607… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-08 (Tue, 08 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- With Pulsar, ensure AMQP consumers receive published messages. Commit: 5bae90156fa7998b575981ac452db21f34683085 https://github.com/galaxyproject/galaxy/commit/5bae90156fa7998b575981ac452d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/util.py Log Message: ----------- Fix a couple flake8 errors including a supposed PEP-8 violation that is actually a PEP-8-suggested acceptable option of how to handle the offending situation. =P Commit: 8778da43cb641a925c421b188aabe053be56e313 https://github.com/galaxyproject/galaxy/commit/8778da43cb641a925c421b188aab… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/manager.py Log Message: ----------- Disable amqp_acknowledge by default, additional fixes from Pulsar's pickier flake8 checks. Commit: ff8e821013e59527bb2bdfacffef2a2db7e562d2 https://github.com/galaxyproject/galaxy/commit/ff8e821013e59527bb2bdfacffef… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/runners/pulsar.py M lib/pulsar/client/action_mapper.py M lib/pulsar/client/amqp_exchange.py M lib/pulsar/client/amqp_exchange_factory.py M lib/pulsar/client/client.py M lib/pulsar/client/config_util.py M lib/pulsar/client/decorators.py M lib/pulsar/client/interface.py M lib/pulsar/client/manager.py M lib/pulsar/client/staging/__init__.py M lib/pulsar/client/staging/down.py M lib/pulsar/client/staging/up.py M lib/pulsar/client/transport/curl.py M lib/pulsar/client/util.py Log Message: ----------- Merge pull request #704 from natefoo/amqp_ack [15.07] With Pulsar, ensure AMQP consumers receive published messages Compare: https://github.com/galaxyproject/galaxy/compare/1203ccc49cbf...ff8e821013e5

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[galaxyproject/usegalaxy-playbook] 18e9a0: Remove Anton and myself from reserved, add Jen
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 18e9a07a40be2036b121e855a9514ebf99cadf28 https://github.com/galaxyproject/usegalaxy-playbook/commit/18e9a07a40be2036… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py Log Message: ----------- Remove Anton and myself from reserved, add Jen

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[galaxyproject/usegalaxy-playbook] 0612fa: Update test to b79555264e6f1d7b042bd5650efeed14832...
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 0612fabefa5e72d4bc5cdcff385591c35a7e462e https://github.com/galaxyproject/usegalaxy-playbook/commit/0612fabefa5e72d4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update test to b79555264e6f1d7b042bd5650efeed1483252095.

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[galaxyproject/galaxy] 54d4c2: Have GenomeSpace tools report the GS tool name (fo...
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 54d4c266bd7c724256f44f0057021d0da2dba3b6 https://github.com/galaxyproject/galaxy/commit/54d4c266bd7c724256f44f005702… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml Log Message: ----------- Have GenomeSpace tools report the GS tool name (for their internal metrics). Default is "Galaxy", but can be overridden by setting "GENOMESPACE_TOOLNAME" environment variable. Commit: b79555264e6f1d7b042bd5650efeed1483252095 https://github.com/galaxyproject/galaxy/commit/b79555264e6f1d7b042bd5650efe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M tools/genomespace/genomespace_exporter.py M tools/genomespace/genomespace_exporter.xml M tools/genomespace/genomespace_file_browser.py M tools/genomespace/genomespace_file_browser_dev.xml M tools/genomespace/genomespace_file_browser_prod.xml M tools/genomespace/genomespace_file_browser_test.xml M tools/genomespace/genomespace_importer.py M tools/genomespace/genomespace_importer.xml Log Message: ----------- Merge pull request #711 from blankenberg/genomespace_toolname Have GenomeSpace tools report the GS tool name Compare: https://github.com/galaxyproject/galaxy/compare/e6a603decec5...b79555264e6f

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[galaxyproject/galaxy] 1e4b40: I think this was broken in #457
by GitHub 10 Sep '15

10 Sep '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e4b4070ce14af06860ee6eb0b963b159097cc39 https://github.com/galaxyproject/galaxy/commit/1e4b4070ce14af06860ee6eb0b96… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- I think this was broken in #457 Commit: e6a603decec5fb3f3b4756c20d0e5cf53700d435 https://github.com/galaxyproject/galaxy/commit/e6a603decec5fb3f3b4756c20d0e… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-09-10 (Thu, 10 Sep 2015) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py Log Message: ----------- Merge pull request #710 from martenson/fix-double-import fix double import for travis Compare: https://github.com/galaxyproject/galaxy/compare/b1b710925a4c...e6a603decec5

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