- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] 5d294e: Fix GFF attribute filtering tool broken in #2983
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5d294ea7d3a14561a15c30f3527dfcd21d517369 https://github.com/galaxyproject/galaxy/commit/5d294ea7d3a14561a15c30f3527d… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Fix GFF attribute filtering tool broken in #2983 Commit: 32bc17cdaa636ba0ba2a97a372b37d518cdd6390 https://github.com/galaxyproject/galaxy/commit/32bc17cdaa636ba0ba2a97a372b3… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Whitespace fix Commit: 0062eacfdf86fbfe8fda3de88b2b5b122cdc567e https://github.com/galaxyproject/galaxy/commit/0062eacfdf86fbfe8fda3de88b2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Merge pull request #3044 from blankenberg/gff-filter-tool-fix Fix GFF attribute filtering tool broken in #2983 Compare: https://github.com/galaxyproject/galaxy/compare/277727ada67d...0062eacfdf86

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[galaxyproject/galaxy] 77f78c: Change __all__ from list to tuple
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 77f78cfbc79ddc345bc22277afc335f11e189491 https://github.com/galaxyproject/galaxy/commit/77f78cfbc79ddc345bc22277afc3… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py M test/unit/tools_support.py M test/unit/unittest_utils/utility.py Log Message: ----------- Change __all__ from list to tuple Also fix import order and Python3 compatibility. Commit: 277727ada67d32404dc953d393716af8aa2aabdc https://github.com/galaxyproject/galaxy/commit/277727ada67d32404dc953d39371… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M lib/galaxy/managers/collections_util.py M lib/galaxy/model/item_attrs.py M lib/galaxy/model/metadata.py M lib/galaxy/model/orm/now.py M lib/galaxy/tools/cwl/__init__.py M lib/galaxy/tools/cwl/cwltool_deps.py M lib/galaxy/tools/cwl/parser.py M lib/galaxy/tools/cwl/runtime_actions.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/mulled/_cli.py M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_channel.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/tools/deps/resolvers/galaxy_packages.py M lib/galaxy/tools/deps/resolvers/homebrew.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py M lib/galaxy/tools/exception_handling.py M lib/galaxy/tools/execute.py M lib/galaxy/tools/loader.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/dataset_matcher.py M lib/galaxy/tools/parameters/wrapped.py M lib/galaxy/tools/parameters/wrapped_json.py M lib/galaxy/tools/parser/__init__.py M lib/galaxy/tools/parser/factory.py M lib/galaxy/tools/toolbox/__init__.py M lib/galaxy/tools/toolbox/lineages/__init__.py M lib/galaxy/tools/toolbox/lineages/factory.py M lib/galaxy/tools/toolbox/lineages/tool_shed.py M lib/galaxy/tools/toolbox/parser.py M lib/galaxy/workflow/extract.py M lib/galaxy/workflow/run.py M lib/galaxy/workflow/schedulers/core.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/api/workflows_format_2/main.py M test/base/driver_util.py M test/unit/tools_support.py M test/unit/unittest_utils/utility.py Log Message: ----------- Merge pull request #3041 from nsoranzo/flake8-import-order Change __all__ from list to tuple [1/2] Compare: https://github.com/galaxyproject/galaxy/compare/36ae57c6e028...277727ada67d

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[galaxyproject/galaxy] f6d5f3: Fix downloading tool tarball with boolean test inp...
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/tool_tarball_fix Home: https://github.com/galaxyproject/galaxy Commit: f6d5f3c4a2e51bd6b75a99dc015360e4ca9a6461 https://github.com/galaxyproject/galaxy/commit/f6d5f3c4a2e51bd6b75a99dc0153… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix downloading tool tarball with boolean test input values.

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[galaxyproject/galaxy] ba0795: Fix tabular filtering tool broken in #2983
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: ba07956117e5e4527fa5d2837da2c267f6ab981d https://github.com/galaxyproject/galaxy/commit/ba07956117e5e4527fa5d2837da2… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/stats/filtering.py Log Message: ----------- Fix tabular filtering tool broken in #2983 Commit: 36ae57c6e028fc814af1cd4740e9222dfcb56021 https://github.com/galaxyproject/galaxy/commit/36ae57c6e028fc814af1cd4740e9… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M tools/stats/filtering.py Log Message: ----------- Merge pull request #3043 from blankenberg/fix-filter-tool Fix tabular filtering tool broken in #2983 Compare: https://github.com/galaxyproject/galaxy/compare/a22a4d0bd5a2...36ae57c6e028

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[galaxyproject/galaxy] 6c17d1: Remove outdated warning
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 6c17d1a823b4367b93fff61d7f2fbed23dc5de3b https://github.com/galaxyproject/galaxy/commit/6c17d1a823b4367b93fff61d7f2f… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Remove outdated warning After digging through the code I am not finding evidence that this was ever possible to do, at least not since sometime pre-2010. Commit: a22a4d0bd5a2376c130ad84e4bc0313b9f252e45 https://github.com/galaxyproject/galaxy/commit/a22a4d0bd5a2376c130ad84e4bc0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-13 (Thu, 13 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- Merge pull request #3046 from erasche/remove_warning Remove outdated warning on ID_SECRET Compare: https://github.com/galaxyproject/galaxy/compare/c6713e7c31d5...a22a4d0bd5a2

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[galaxyproject/galaxy] dcde64: Fix import order. Fix typos and improve readabilit...
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dcde64ce407b332072525c66885adf03a26eeb5e https://github.com/galaxyproject/galaxy/commit/dcde64ce407b332072525c66885a… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/workflow/extract.py M test/api/test_workflow_extraction.py Log Message: ----------- Fix import order. Fix typos and improve readability Commit: 04bf2153b8f61c60288cb180d448e7c20352f6e7 https://github.com/galaxyproject/galaxy/commit/04bf2153b8f61c60288cb180d448… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M lib/galaxy/workflow/extract.py Log Message: ----------- WorkflowSummary: add dict to map a job id to its representative job Fix #2742 introduced in commit 9ede8e556be1f6038361b579c1457068e50e951a . The representative job is the first in the returned query, so substantially random and not necessarily the one with the lowest job id. Mapping a job id to its representative job in extract_steps() makes it robust also against API requests with manually chosen collection job ids. Commit: c6713e7c31d5ffe576af5af7de56d3536d196786 https://github.com/galaxyproject/galaxy/commit/c6713e7c31d5ffe576af5af7de56… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M .ci/flake8_lint_include_list.txt M lib/galaxy/workflow/extract.py M test/api/test_workflow_extraction.py Log Message: ----------- Merge pull request #3039 from nsoranzo/fix_for_2742 Fix workflow extraction API tests on PostgreSQL Compare: https://github.com/galaxyproject/galaxy/compare/1e2688f15785...c6713e7c31d5

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[galaxyproject/galaxy] 91bfec: Add documentation on optional ``multiple="true"`` ...
by GitHub 13 Oct '16

13 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 91bfecea67b78f7e459a250a7844c6344154367f https://github.com/galaxyproject/galaxy/commit/91bfecea67b78f7e459a250a7844… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Add documentation on optional ``multiple="true"`` data parameters. Thanks to detailed biostar question from @lindenb (sorry these parameters are so counter-intuitive - I don't have an excuse other than a need to preserve backward compatibility). Rebased with indention requested by @nsoranzo and fixes for the test case tool. Commit: 1e2688f1578552ea03e7a601d927c4475b96fdd2 https://github.com/galaxyproject/galaxy/commit/1e2688f1578552ea03e7a601d927… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M lib/galaxy/tools/xsd/galaxy.xsd A test/functional/tools/multi_data_optional.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Merge pull request #3024 from jmchilton/multi_optional_param Add documentation on optional ``multiple="true"`` data parameters. Compare: https://github.com/galaxyproject/galaxy/compare/58d608b9060d...1e2688f15785

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[galaxyproject/usegalaxy-playbook] 15ce7b: Added 2 hour expiration to welcome images
by GitHub 12 Oct '16

12 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 15ce7b388961f5602cb73ea3ef86369b9353bac4 https://github.com/galaxyproject/usegalaxy-playbook/commit/15ce7b388961f560… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M templates/nginx/galaxy_test.j2 M templates/nginx/usegalaxy.j2 Log Message: ----------- Added 2 hour expiration to welcome images

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[galaxyproject/usegalaxy-playbook] f5e6cf: Increase the job output limit to 200GB
by GitHub 12 Oct '16

12 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f5e6cf2545cabc406008bc52c378a51683b39859 https://github.com/galaxyproject/usegalaxy-playbook/commit/f5e6cf2545cabc40… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-12 (Wed, 12 Oct 2016) Changed paths: M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Increase the job output limit to 200GB

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[galaxyproject/usegalaxy-playbook] b75611: Fix gzip content encoding regressions for Test/Mai...
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b75611579b5fd15ff8b1f8d219e1b2daddb6b481 https://github.com/galaxyproject/usegalaxy-playbook/commit/b75611579b5fd15f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M common/host_vars/radegast.galaxyproject.org.yml M production/group_vars/galaxywebservers.yml M stage/group_vars/galaxyservers.yml M templates/nginx/galaxy_test.j2 M templates/nginx/toolshed.j2 M templates/nginx/usegalaxy.j2 Log Message: ----------- Fix gzip content encoding regressions for Test/Main and Toolsheds

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[galaxyproject/usegalaxy-playbook] 77b45f: Update nginx gzip_types
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 77b45fea07c7d42544f3144d4058028ec61ec83e https://github.com/galaxyproject/usegalaxy-playbook/commit/77b45fea07c7d425… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M common_roles M production/group_vars/galaxywebservers.yml M stage/group_vars/galaxyservers.yml Log Message: ----------- Update nginx gzip_types

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[galaxyproject/usegalaxy-playbook] 588ad4: Main update, plus Nagios monitoring for Jetstream ...
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 588ad48433572a524f961952af9fc7fe059f8632 https://github.com/galaxyproject/usegalaxy-playbook/commit/588ad48433572a52… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M files/galaxy/test.galaxyproject.org/config/nagios_tool_conf.xml A files/galaxy/test.galaxyproject.org/nagios/echo_test_bridges.xml R files/galaxy/test.galaxyproject.org/nagios/echo_test_greenfield.xml A files/galaxy/test.galaxyproject.org/nagios/echo_test_jetstream_iu.xml A files/galaxy/test.galaxyproject.org/nagios/echo_test_jetstream_tacc.xml M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml M files/galaxy/usegalaxy.org/config/nagios_tool_conf.xml A files/galaxy/usegalaxy.org/nagios/echo_main_bridges.xml A files/galaxy/usegalaxy.org/nagios/echo_main_jetstream_iu.xml A files/galaxy/usegalaxy.org/nagios/echo_main_jetstream_tacc.xml M files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml M files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml M galaxy.yml M production/galaxy_version.yml M production/group_vars/galaxyservers.yml M stage/galaxy_version.yml M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/job_conf.xml.j2 Log Message: ----------- Main update, plus Nagios monitoring for Jetstream and Bridges

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[galaxyproject/usegalaxy-playbook] 9a68c4: update MTS to altest master-toolshed
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9a68c490dbb406aa50bf14e04f14c13b8d34b1a8 https://github.com/galaxyproject/usegalaxy-playbook/commit/9a68c490dbb406aa… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M common_roles M production/group_vars/toolshedservers.yml Log Message: ----------- update MTS to altest master-toolshed updat subrepo

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[galaxyproject/galaxy] b83f0a: Fix whoosh indexing.
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/master-toolshed Home: https://github.com/galaxyproject/galaxy Commit: b83f0a10247119ef18bf72688d4e0bb8cfee8e36 https://github.com/galaxyproject/galaxy/commit/b83f0a10247119ef18bf72688d4e… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-21 (Wed, 21 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Fix whoosh indexing. Commit: d7ab1c5cfbfcdff3ce3e201f6fb0684fdb914096 https://github.com/galaxyproject/galaxy/commit/d7ab1c5cfbfcdff3ce3e201f6fb0… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- UI, Modal: re-build dom on render Moves templating to render (and updates dom node attributes after) to reset modal and prevent inline styling and other modifications to the singleton from persisting between calls to show. Commit: 9b3c061addb4f3e61d72465cf492396b9e07464e https://github.com/galaxyproject/galaxy/commit/9b3c061addb4f3e61d72465cf492… Author: Dave B <dave(a)bx.psu.edu> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py Log Message: ----------- [16.07] Fix tool dependencies handling in Tool Shed model (#2950) * Fix the cause of toolshed test 1400 failing. * Fix handling of repositories without tool dependencies. * Fix tool dependency retrieval. In some cases, a process might attempt to fetch tool dependencies for revision 1:7334f6d0ac17, but the repository has been updated, and tool dependency metadata has been reassigned to e.g. 7:ce22ceec214a. This commit resolves that issue. * Correct the logic that returns an empty string for an empty dict. * Fix getting latest revision with tool dependencies. * Use self.app instead of trans.app Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py Commit: a78b8bcd2aa02abf787f0974fe567ab4f70f41a1 https://github.com/galaxyproject/galaxy/commit/a78b8bcd2aa02abf787f0974fe56… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: A lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py M lib/galaxy/managers/rbac_secured.py M test/unit/managers/test_DatasetManager.py Log Message: ----------- Merge branch 'release_16.04' of https://github.com/galaxyproject/galaxy into release_16.04 Commit: e18d4ed33b8b453229f969f2d05c997b2fa7fe96 https://github.com/galaxyproject/galaxy/commit/e18d4ed33b8b453229f969f2d05c… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- UI, datasets: fix optional column form values Updates metadata column checkbox flag from 'true' to '__NOTHING__' to reflect newer form_builder values. Fixes #2175 Commit: aa2e7834f697f02ebf11545b53882baee8b87f4e https://github.com/galaxyproject/galaxy/commit/aa2e7834f697f02ebf11545b5388… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Fix optional flag for library datasets in legacy library ui Commit: c06f8c29968971c6c1e0dfc6847b3baf755f3a96 https://github.com/galaxyproject/galaxy/commit/c06f8c29968971c6c1e0dfc6847b… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- correct the method call Commit: 5e7ee28e0d6937fa53f39b350e04357b554ce9ae https://github.com/galaxyproject/galaxy/commit/5e7ee28e0d6937fa53f39b350e04… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-22 (Thu, 22 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- bump freebayes in test (since it was updated) Commit: 45e6949eeae88c0d3c4c3f6341ddc5695d329bb2 https://github.com/galaxyproject/galaxy/commit/45e6949eeae88c0d3c4c3f6341dd… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/webapps/tool_shed/model/__init__.py M lib/tool_shed/util/metadata_util.py M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge pull request #2959 from martenson/release_16.04 [16.04] backport of model tool dependencies fix Commit: 2c8a5d9d58c49c662aed4193f71caaf3fafe5651 https://github.com/galaxyproject/galaxy/commit/2c8a5d9d58c49c662aed4193f71c… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Correct import order. Commit: 3b3e2e3358aa73a5374345686581310d37349ff9 https://github.com/galaxyproject/galaxy/commit/3b3e2e3358aa73a5374345686581… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Conflicts: lib/galaxy/webapps/tool_shed/controllers/repository.py lib/galaxy/webapps/tool_shed/model/__init__.py Commit: 092a7307c21afa8d66129dca23567b49a540d66a https://github.com/galaxyproject/galaxy/commit/092a7307c21afa8d66129dca2356… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-09-23 (Fri, 23 Sep 2016) Changed paths: M scripts/tool_shed/build_ts_whoosh_index.py Log Message: ----------- Merge pull request #2949 from davebx/backport_whoosh [16.07] Fix missing import in whoosh indexing script Commit: 26d381c9a5d77ecfa6bf3e96b2cb77df3d3f846d https://github.com/galaxyproject/galaxy/commit/26d381c9a5d77ecfa6bf3e96b2cb… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-24 (Sat, 24 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/library_common.py Log Message: ----------- Merge pull request #2962 from guerler/fix_library_optional_flag [16.07] Fix optional flag for library datasets in legacy library ui Commit: e667f9f360388839d723421b884836acb6974e6c https://github.com/galaxyproject/galaxy/commit/e667f9f360388839d723421b8848… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-09-25 (Sun, 25 Sep 2016) Changed paths: M lib/galaxy/webapps/galaxy/controllers/dataset.py Log Message: ----------- Merge pull request #2960 from carlfeberhard/fix.bed-columns [16.07] UI, datasets: fix optional column form values Commit: 04d62e242412d0eb6e739f3577256d99b1aaa5bf https://github.com/galaxyproject/galaxy/commit/04d62e242412d0eb6e739f357725… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-09-26 (Mon, 26 Sep 2016) Changed paths: M client/galaxy/scripts/mvc/ui/ui-modal.js M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js Log Message: ----------- Merge pull request #2955 from carlfeberhard/fix.modal-resetting [16.07] UI, Modal: re-build dom on render Commit: 375ed8cc81590a18a52b61e32307562488fd551e https://github.com/galaxyproject/galaxy/commit/375ed8cc81590a18a52b61e32307… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- polish resolvers section in conda faq docs Commit: ba274e37f2f0e8c9973b19c46fe99c5565c5118c https://github.com/galaxyproject/galaxy/commit/ba274e37f2f0e8c9973b19c46fe9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- describe the conda installation behavior a bit better Commit: 2899372791fdbba4f8db7c414a5447cf049987f3 https://github.com/galaxyproject/galaxy/commit/2899372791fdbba4f8db7c414a54… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Update conda_faq.rst Commit: fdfe9d8c20a63e6e6e6951d5fe5cbd7d74446d0a https://github.com/galaxyproject/galaxy/commit/fdfe9d8c20a63e6e6e6951d5fe5c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #19 from martenson/nsoranzo-patch-1-1 Small fixes to conda_faq.rst changes Commit: d9fab3345856770a16a98f18cf9e6185a4eae91a https://github.com/galaxyproject/galaxy/commit/d9fab3345856770a16a98f18cf9e… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-10-03 (Mon, 03 Oct 2016) Changed paths: M doc/source/admin/conda_faq.rst Log Message: ----------- Merge pull request #2998 from martenson/conda-faq-polish [16.07] Conda FAQ polish Commit: 1e8337df5a4acf9e899adc07883f967973cbcac7 https://github.com/galaxyproject/galaxy/commit/1e8337df5a4acf9e899adc07883f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix setting conda_copy_dependencies in galaxy.ini. (cherry picked from commit 9246b8629c3831ab623983c9003c4e92cbde97d5) Commit: 6d27a3c4b6184b393e535afd32f87e55e7a07b70 https://github.com/galaxyproject/galaxy/commit/6d27a3c4b6184b393e535afd32f8… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Fix initial conda version at 4.0.5 This should prevent missing `activate` in <conda_prefix>/bin when downgrading to 3.19.3. This is what the conda people use in their CI environment ( [see](https://github.com/conda/conda/blob/master/utils/travis-run-install.sh… and perhaps why that bug made it into the release in the first place). Commit: f7c3e25e5db1a1d99c81380f552719bee07c1790 https://github.com/galaxyproject/galaxy/commit/f7c3e25e5db1a1d99c81380f5527… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge pull request #3009 from mvdbeek/conda_downgrade [16.01] Backport #2869 Fix initial conda version at 4.0.5 Commit: 224c2126c73617ec906abc1e08d5f5a7548633b1 https://github.com/galaxyproject/galaxy/commit/224c2126c73617ec906abc1e08d5… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.01' into release_16.04 Commit: d6845c249466d013b58ab021540fc5176096aaa0 https://github.com/galaxyproject/galaxy/commit/d6845c249466d013b58ab021540f… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/conda_util.py Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: f32b6446a7a4fd5a0bca2fa8e93d4407e0ce3938 https://github.com/galaxyproject/galaxy/commit/f32b6446a7a4fd5a0bca2fa8e93d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-05 (Wed, 05 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3008 from natefoo/conda-copy-dependencies [16.07] Fix setting conda_copy_dependencies in galaxy.ini. Commit: 89278b0ec70b7a8f1cf42bda87335cf4f98f175b https://github.com/galaxyproject/galaxy/commit/89278b0ec70b7a8f1cf42bda8733… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix for bioconda recipes depending on conda-forge. Some bioconda recipes now depend on conda forge, this fix is needed for them to work properly. Commit: ddacf38a11a9f752b3cfe13a8b63182ff1d02d06 https://github.com/galaxyproject/galaxy/commit/ddacf38a11a9f752b3cfe13a8b63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3023 from jmchilton/fix_abyss [16.07] Fix for bioconda recipes depending on conda-forge. Commit: 39fb030f13c45991d4a2ca811b66e7872fb0a4e7 https://github.com/galaxyproject/galaxy/commit/39fb030f13c45991d4a2ca811b66… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Remove travis-ci python installation, since python2.7 is preinstalled on OSX images now Commit: 2adb98e58cc0f1d0d25aecc260d7108902d4b02c https://github.com/galaxyproject/galaxy/commit/2adb98e58cc0f1d0d25aecc260d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #3034 from mvdbeek/skip_python_install_travis [16.04] Remove travis-ci python installation, since python2.7 is preinstalled… Commit: 3300a73c9db6b99cbec6ae952e3e59f8a72e651b https://github.com/galaxyproject/galaxy/commit/3300a73c9db6b99cbec6ae952e3e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 735c682ead5f97ef150632b3ecc4d8d9bd593a33 https://github.com/galaxyproject/galaxy/commit/735c682ead5f97ef150632b3ecc4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml M client/galaxy/scripts/mvc/ui/ui-modal.js M config/galaxy.ini.sample M doc/source/admin/conda_faq.rst M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/resolvers/conda.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M scripts/tool_shed/build_ts_whoosh_index.py M static/maps/mvc/ui/ui-modal.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/ui/ui-modal.js M test/shed_functional/functional/test_1400_review_migration_stages.py Log Message: ----------- Merge pull request #3037 from galaxyproject/release_16.07 [master-toolshed] merge-in release_16.07 changes Compare: https://github.com/galaxyproject/galaxy/compare/673a9a3a5b55...735c682ead5f

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[galaxyproject/usegalaxy-playbook] eae65b: Increase shared_buffers for galaxy-db-01
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: eae65b46a3cf9d3133b94ce3ef56841afb57c617 https://github.com/galaxyproject/usegalaxy-playbook/commit/eae65b46a3cf9d31… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M common/host_vars/galaxy-db-01.tacc.utexas.edu.yml Log Message: ----------- Increase shared_buffers for galaxy-db-01

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[galaxyproject/galaxy] 2b9281: Fix dependency ordering broken in #2917.
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2b9281a37832346b0a3e5aed1b13ee84270ffe44 https://github.com/galaxyproject/galaxy/commit/2b9281a37832346b0a3e5aed1b13… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Fix dependency ordering broken in #2917. We will store dependencies in an OrderedDict, matching the order of `<requirements>`. Fixes an issue where an R library was being sourced before R itself during shell command generation, the sourcing of R afterwards overwrote the `R_LIBS` env setting. Commit: 58d608b9060d7608c33d711183790e3b19c313cc https://github.com/galaxyproject/galaxy/commit/58d608b9060d7608c33d71118379… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/tools/deps/__init__.py Log Message: ----------- Merge pull request #3036 from blankenberg/fix-dep-shell-order Fix dependency ordering broken in #2917. Compare: https://github.com/galaxyproject/galaxy/compare/115600673300...58d608b9060d

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[galaxyproject/galaxy] 89278b: Fix for bioconda recipes depending on conda-forge.
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89278b0ec70b7a8f1cf42bda87335cf4f98f175b https://github.com/galaxyproject/galaxy/commit/89278b0ec70b7a8f1cf42bda8733… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix for bioconda recipes depending on conda-forge. Some bioconda recipes now depend on conda forge, this fix is needed for them to work properly. Commit: ddacf38a11a9f752b3cfe13a8b63182ff1d02d06 https://github.com/galaxyproject/galaxy/commit/ddacf38a11a9f752b3cfe13a8b63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3023 from jmchilton/fix_abyss [16.07] Fix for bioconda recipes depending on conda-forge. Commit: 39fb030f13c45991d4a2ca811b66e7872fb0a4e7 https://github.com/galaxyproject/galaxy/commit/39fb030f13c45991d4a2ca811b66… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Remove travis-ci python installation, since python2.7 is preinstalled on OSX images now Commit: 2adb98e58cc0f1d0d25aecc260d7108902d4b02c https://github.com/galaxyproject/galaxy/commit/2adb98e58cc0f1d0d25aecc260d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #3034 from mvdbeek/skip_python_install_travis [16.04] Remove travis-ci python installation, since python2.7 is preinstalled… Commit: 3300a73c9db6b99cbec6ae952e3e59f8a72e651b https://github.com/galaxyproject/galaxy/commit/3300a73c9db6b99cbec6ae952e3e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Commit: 1156006733001fb06520a70f54a9227f5b4c7061 https://github.com/galaxyproject/galaxy/commit/1156006733001fb06520a70f54a9… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst Log Message: ----------- Merge branch 'release_16.07' into dev Conflicts: lib/galaxy/tools/deps/__init__.py Compare: https://github.com/galaxyproject/galaxy/compare/6639a181df3b...115600673300

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[galaxyproject/galaxy] 39fb03: Remove travis-ci python installation, since python...
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 39fb030f13c45991d4a2ca811b66e7872fb0a4e7 https://github.com/galaxyproject/galaxy/commit/39fb030f13c45991d4a2ca811b66… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Remove travis-ci python installation, since python2.7 is preinstalled on OSX images now Commit: 2adb98e58cc0f1d0d25aecc260d7108902d4b02c https://github.com/galaxyproject/galaxy/commit/2adb98e58cc0f1d0d25aecc260d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #3034 from mvdbeek/skip_python_install_travis [16.04] Remove travis-ci python installation, since python2.7 is preinstalled… Commit: 3300a73c9db6b99cbec6ae952e3e59f8a72e651b https://github.com/galaxyproject/galaxy/commit/3300a73c9db6b99cbec6ae952e3e… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge branch 'release_16.04' into release_16.07 Compare: https://github.com/galaxyproject/galaxy/compare/ddacf38a11a9...3300a73c9db6

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[galaxyproject/galaxy] 39fb03: Remove travis-ci python installation, since python...
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/release_16.04 Home: https://github.com/galaxyproject/galaxy Commit: 39fb030f13c45991d4a2ca811b66e7872fb0a4e7 https://github.com/galaxyproject/galaxy/commit/39fb030f13c45991d4a2ca811b66… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Remove travis-ci python installation, since python2.7 is preinstalled on OSX images now Commit: 2adb98e58cc0f1d0d25aecc260d7108902d4b02c https://github.com/galaxyproject/galaxy/commit/2adb98e58cc0f1d0d25aecc260d7… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M .travis.yml Log Message: ----------- Merge pull request #3034 from mvdbeek/skip_python_install_travis [16.04] Remove travis-ci python installation, since python2.7 is preinstalled… Compare: https://github.com/galaxyproject/galaxy/compare/224c2126c736...2adb98e58cc0

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[galaxyproject/galaxy] 415c7f: Verify tools coming from cache have correct id.
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 415c7fa67be28885fa92246fb63efdf5bfd777bf https://github.com/galaxyproject/galaxy/commit/415c7fa67be28885fa92246fb63e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Verify tools coming from cache have correct id. Commit: 56dfaf003f3239d2475715b478e319ff359e08d4 https://github.com/galaxyproject/galaxy/commit/56dfaf003f3239d2475715b478e3… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-10-08 (Sat, 08 Oct 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Fix tool reload in 415c7fa67be28885fa92246fb63efdf5bfd777bf Previous commit changed the if/elif/else logic. The else was now applying also to cached tools, which it should not. Instead, explicitly check that we still don't have a tool object. Commit: 6639a181df3ba8f2a26e6a9bde27e53866cf110a https://github.com/galaxyproject/galaxy/commit/6639a181df3ba8f2a26e6a9bde27… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-10-11 (Tue, 11 Oct 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #3025 from mvdbeek/cache_fix Cache fix Compare: https://github.com/galaxyproject/galaxy/compare/191bae9a2b9d...6639a181df3b

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[galaxyproject/galaxy] fad562: Datatypes: include base classes in search by name
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fad562876f886e3384fec1a9782685251d12e2c1 https://github.com/galaxyproject/galaxy/commit/fad562876f886e3384fec1a97826… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Datatypes: include base classes in search by name Fixes #2982 Adds the base class 'images.Image' to the list of classes returnable by 'datatypes_registry.get_datatype_class_by_name'. Normally that method searches the registry's list of datatypes and those are instantiable classes only. The images.Image can be considered an abstract base class and you'd never create a dataset of that datatype. The method is used for getting classes for 'isinstance' tests, however, so including base classes like 'images.Image' allow testing for all its image subclasses. This change makes that possible and allows the method (and its consumers) to behave in a much more predictable and useful manner. Commit: 191bae9a2b9d06bb7d461633b0a43ce320a042c4 https://github.com/galaxyproject/galaxy/commit/191bae9a2b9d06bb7d461633b0a4… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Merge pull request #3028 from carlfeberhard/fix.tiff Datatypes: include base classes in search by name Compare: https://github.com/galaxyproject/galaxy/compare/75d1f8496acc...191bae9a2b9d

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[galaxyproject/galaxy] 1e32c0: Fix import order and Python3 compatibility for mos...
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1e32c0926ca3fcee79f355577c5525c4bf73c8e4 https://github.com/galaxyproject/galaxy/commit/1e32c0926ca3fcee79f355577c55… Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/style/source_material/circle.py M doc/parse_gx_xsd.py M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py Log Message: ----------- Fix import order and Python3 compatibility for most of test/ Commit: 75d1f8496acc060e8bd91cdaffd082fc9685ef1f https://github.com/galaxyproject/galaxy/commit/75d1f8496acc060e8bd91cdaffd0… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M client/galaxy/style/source_material/circle.py M doc/parse_gx_xsd.py M test/api/helpers.py M test/api/test_api_batch.py M test/api/test_authenticate.py M test/api/test_dataset_collections.py M test/api/test_history_contents.py M test/api/test_page_revisions.py M test/api/test_pages.py M test/api/test_tool_data.py M test/api/test_tools.py M test/api/test_users.py M test/api/test_workflow_extraction.py M test/api/test_workflows.py M test/api/workflows_format_2/__init__.py M test/api/workflows_format_2/converter.py M test/base/api.py M test/base/driver_util.py M test/base/integration_util.py M test/base/interactor.py M test/base/test_logging.py M test/base/twilltestcase.py M test/functional/test_data_managers.py M test/functional/test_library_templates.py M test/functional/test_toolbox.py M test/functional/workflow.py M test/integration/test_resolvers.py M test/manual/workflows_scaling.py M test/shed_functional/base/test_db_util.py M test/shed_functional/functional/test_0300_reset_all_metadata.py M test/shed_functional/functional/test_1300_reset_all_metadata.py M test/shed_functional/functional_tests.py Log Message: ----------- Merge pull request #3031 from nsoranzo/flake8-import-order Fix import order and Python3 compatibility for most of test/ Compare: https://github.com/galaxyproject/galaxy/compare/7d642c063f18...75d1f8496acc

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[galaxyproject/galaxy] 1a2d75: add muled docs to admin index
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 1a2d75fade1077359b2a9b1072feab793022b7f4 https://github.com/galaxyproject/galaxy/commit/1a2d75fade1077359b2a9b1072fe… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M doc/source/admin/index.rst Log Message: ----------- add muled docs to admin index Commit: 7d642c063f18b18b438a4840705f09652f3b586d https://github.com/galaxyproject/galaxy/commit/7d642c063f18b18b438a4840705f… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M doc/source/admin/index.rst Log Message: ----------- Merge pull request #3032 from martenson/link-mulled-docs add muled docs to admin index Compare: https://github.com/galaxyproject/galaxy/compare/7db241faa6d5...7d642c063f18

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[galaxyproject/galaxy] 5a7244: Implement beta support for dynamically discovering...
by GitHub 11 Oct '16

11 Oct '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 5a72449246be6f0f2fe3955bebf6f42ae89966bc https://github.com/galaxyproject/galaxy/commit/5a72449246be6f0f2fe3955bebf6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-08 (Sat, 08 Oct 2016) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml Log Message: ----------- Implement beta support for dynamically discovering mulled containers for dependencies. Contains all mulled fixes and enhancements through 16.10.7 including several bug fixes from @bgruening. Commit: e389e1939160dfef7c364785a17869f5de30198b https://github.com/galaxyproject/galaxy/commit/e389e1939160dfef7c364785a178… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-08 (Sat, 08 Oct 2016) Changed paths: M config/job_conf.xml.sample_advanced M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M test/unit/jobs/test_runner_local.py Log Message: ----------- Implement option to require containerization of jobs. This is great for security in production. For my own greedy concerns, I'm adding it for development however. I don't want someone to be testing mulled containers and accidently run the job locally. Commit: 654b5e9322f5c54332c8d8861bc8ed34c6e71a8e https://github.com/galaxyproject/galaxy/commit/654b5e9322f5c54332c8d8861bc8… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-09 (Sun, 09 Oct 2016) Changed paths: A doc/source/admin/mulled_containers.rst Log Message: ----------- Add initial documentation about the new mulled features. Commit: 4b5114bed1c09c655654972b084274e74310ebe8 https://github.com/galaxyproject/galaxy/commit/4b5114bed1c09c655654972b0842… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: A doc/source/admin/mulled_containers.rst Log Message: ----------- Merge pull request #50 from jmchilton/mulled_docs Add initial documentation about the new mulled features. Commit: f0b988da78f081bf6845ce2d280d153e221f3633 https://github.com/galaxyproject/galaxy/commit/f0b988da78f081bf6845ce2d280d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/util.py Log Message: ----------- Bring in latest galaxy-lib fixes. Commit: 20dcc4d693ae8fa7e846eb32e65292c3c4a38863 https://github.com/galaxyproject/galaxy/commit/20dcc4d693ae8fa7e846eb32e652… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M config/galaxy.ini.sample Log Message: ----------- remove duplicated option from config sample Commit: bcabbd8707e0064e041e730e5abd1d8dfc0a692c https://github.com/galaxyproject/galaxy/commit/bcabbd8707e0064e041e730e5abd… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M doc/source/admin/mulled_containers.rst Log Message: ----------- minor changes to mulled admin docs Commit: 7db241faa6d505427108c5ddeae8dbc77c384613 https://github.com/galaxyproject/galaxy/commit/7db241faa6d505427108c5ddeae8… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M config/galaxy.ini.sample M config/job_conf.xml.sample_advanced A doc/source/admin/mulled_containers.rst M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/__init__.py M lib/galaxy/tools/deps/__init__.py A lib/galaxy/tools/deps/conda_compat.py M lib/galaxy/tools/deps/conda_util.py A lib/galaxy/tools/deps/container_resolvers/__init__.py A lib/galaxy/tools/deps/container_resolvers/explicit.py A lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py A lib/galaxy/tools/deps/installable.py A lib/galaxy/tools/deps/mulled/__init__.py A lib/galaxy/tools/deps/mulled/_cli.py A lib/galaxy/tools/deps/mulled/invfile.lua A lib/galaxy/tools/deps/mulled/mulled_build.py A lib/galaxy/tools/deps/mulled/mulled_build_channel.py A lib/galaxy/tools/deps/mulled/mulled_build_files.py A lib/galaxy/tools/deps/mulled/mulled_build_tool.py A lib/galaxy/tools/deps/mulled/mulled_search.py A lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/deps/resolvers/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py A test/functional/tools/mulled_example_multi_1.xml M test/functional/tools/samples_tool_conf.xml M test/unit/jobs/test_runner_local.py Log Message: ----------- Merge pull request #2986 from jmchilton/mulled Implement beta support for discovering mulled containers for dependencies. Compare: https://github.com/galaxyproject/galaxy/compare/217854827ac7...7db241faa6d5

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[galaxyproject/galaxy] 89278b: Fix for bioconda recipes depending on conda-forge.
by GitHub 10 Oct '16

10 Oct '16

Branch: refs/heads/release_16.07 Home: https://github.com/galaxyproject/galaxy Commit: 89278b0ec70b7a8f1cf42bda87335cf4f98f175b https://github.com/galaxyproject/galaxy/commit/89278b0ec70b7a8f1cf42bda8733… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-10-07 (Fri, 07 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Fix for bioconda recipes depending on conda-forge. Some bioconda recipes now depend on conda forge, this fix is needed for them to work properly. Commit: ddacf38a11a9f752b3cfe13a8b63182ff1d02d06 https://github.com/galaxyproject/galaxy/commit/ddacf38a11a9f752b3cfe13a8b63… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-10-10 (Mon, 10 Oct 2016) Changed paths: M config/galaxy.ini.sample M doc/source/admin/dependency_resolvers.rst M lib/galaxy/tools/deps/__init__.py M lib/galaxy/tools/deps/resolvers/conda.py Log Message: ----------- Merge pull request #3023 from jmchilton/fix_abyss [16.07] Fix for bioconda recipes depending on conda-forge. Compare: https://github.com/galaxyproject/galaxy/compare/f32b6446a7a4...ddacf38a11a9

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