- galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] b3e939: Replace get_tool_shed_repository_by_tool_shed_name...
by GitHub 15 Mar '16

15 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b3e9398c3affa964fdc8cf090eb5c149f7a6bf47 https://github.com/galaxyproject/galaxy/commit/b3e9398c3affa964fdc8cf090eb5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship Commit: d6e38c7d482eae65fc135cd65a13b7f215220cd5 https://github.com/galaxyproject/galaxy/commit/d6e38c7d482eae65fc135cd65a13… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- remove unused import Commit: 5a50a4691c11edb9366f2e0d3eeb68aaaabb9c80 https://github.com/galaxyproject/galaxy/commit/5a50a4691c11edb9366f2e0d3eeb… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Merge pull request #1909 from mvdbeek/backport_repository_for_dependency_relationship [16.01] Backport PR #1868 Commit: 90fcd8c668865ce109b3fbc011319a9794e9e47f https://github.com/galaxyproject/galaxy/commit/90fcd8c668865ce109b3fbc01131… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-14 (Mon, 14 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Handle sections in view workflow Fixes 1723 Commit: 65a5b08c7129462a310fc741fb64e7f883bd8b0f https://github.com/galaxyproject/galaxy/commit/65a5b08c7129462a310fc741fb64… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #1916 from erasche/fix-1723-back [16.01] Handle sections in view workflow Commit: 18473a187e019421933746abb31f8b226e828b80 https://github.com/galaxyproject/galaxy/commit/18473a187e019421933746abb31f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Ensure chrom, start, end as bytestring in BamDataProvider Commit: 9a343efe8b7dd393842e0f971e59d575f2286de2 https://github.com/galaxyproject/galaxy/commit/9a343efe8b7dd393842e0f971e59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #1930 from mvdbeek/more_bytestring_for_pysam [16.01] Ensure chrom, start, end as bytestring in BamDataProvider Commit: 9a0f971596a37726acc75f7e8c9ec6c947c5dce6 https://github.com/galaxyproject/galaxy/commit/9a0f971596a37726acc75f7e8c9e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/23c33009001f...9a0f971596a3

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[galaxyproject/galaxy] 18473a: Ensure chrom, start, end as bytestring in BamDataP...
by GitHub 15 Mar '16

15 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 18473a187e019421933746abb31f8b226e828b80 https://github.com/galaxyproject/galaxy/commit/18473a187e019421933746abb31f… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Ensure chrom, start, end as bytestring in BamDataProvider Commit: 9a343efe8b7dd393842e0f971e59d575f2286de2 https://github.com/galaxyproject/galaxy/commit/9a343efe8b7dd393842e0f971e59… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #1930 from mvdbeek/more_bytestring_for_pysam [16.01] Ensure chrom, start, end as bytestring in BamDataProvider Compare: https://github.com/galaxyproject/galaxy/compare/65a5b08c7129...9a343efe8b7d

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[galaxyproject/galaxy] 90fcd8: Handle sections in view workflow
by GitHub 15 Mar '16

15 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 90fcd8c668865ce109b3fbc011319a9794e9e47f https://github.com/galaxyproject/galaxy/commit/90fcd8c668865ce109b3fbc01131… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-14 (Mon, 14 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Handle sections in view workflow Fixes 1723 Commit: 65a5b08c7129462a310fc741fb64e7f883bd8b0f https://github.com/galaxyproject/galaxy/commit/65a5b08c7129462a310fc741fb64… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/display.mako Log Message: ----------- Merge pull request #1916 from erasche/fix-1723-back [16.01] Handle sections in view workflow Compare: https://github.com/galaxyproject/galaxy/compare/5a50a4691c11...65a5b08c7129

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[galaxyproject/usegalaxy-playbook] 65111e: Dropped Gxycast 1 2015 slide.
by GitHub 14 Mar '16

14 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 65111e37d7f4373b111869e37041f87b49f60465 https://github.com/galaxyproject/usegalaxy-playbook/commit/65111e37d7f4373b… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-03-14 (Mon, 14 Mar 2016) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped Gxycast 1 2015 slide.

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[galaxyproject/galaxy] 069736: adding contrib init for reports and modifying stat...
by GitHub 14 Mar '16

14 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 0697364f9df3f62a7f9d4f3d98939b442c597965 https://github.com/galaxyproject/galaxy/commit/0697364f9df3f62a7f9d4f3d9893… Author: Mikael Loaec <mikael.loaec(a)versailles.inra.fr> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init Log Message: ----------- adding contrib init for reports and modifying status check to have output by process in case multiprocess Commit: 6d6b63729939125c5b1cb9c1ccc356192ace90fe https://github.com/galaxyproject/galaxy/commit/6d6b63729939125c5b1cb9c1ccc3… Author: Mikael Loaec <mikael.loaec(a)versailles.inra.fr> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M contrib/galaxy.fedora-init M contrib/galaxy_reports.fedora-init Log Message: ----------- removing lock files creation and deletion because of rigths problems in case of using galaxy user Commit: d9c00771d0dd331f18fa38b6db34b7ec1fa0500e https://github.com/galaxyproject/galaxy/commit/d9c00771d0dd331f18fa38b6db34… Author: Mikael Loaec <mikael.loaec(a)versailles.inra.fr> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M contrib/galaxy.fedora-init Log Message: ----------- adding blank line to separate function Commit: 1aaf65e8b6306e3d4a7e69d545d9fe300c1510ca https://github.com/galaxyproject/galaxy/commit/1aaf65e8b6306e3d4a7e69d545d9… Author: Mikael Loaec <mikael.loaec(a)versailles.inra.fr> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M contrib/galaxy_reports.fedora-init Log Message: ----------- missing ;; in case stop Commit: 23c33009001facff4ec45baa1e8d228b3cef6860 https://github.com/galaxyproject/galaxy/commit/23c33009001facff4ec45baa1e8d… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2016-03-14 (Mon, 14 Mar 2016) Changed paths: M contrib/galaxy.fedora-init A contrib/galaxy_reports.fedora-init Log Message: ----------- Merge pull request #1911 from miloaec/dev adding contrib init for reports and modifying status check to have ou… Compare: https://github.com/galaxyproject/galaxy/compare/ff0bcd392015...23c33009001f

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[galaxyproject/galaxy] 14d6e3: Rename from_html to from_json
by GitHub 14 Mar '16

14 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 14d6e34e010cafd98d8db2680c4c339e727c968d https://github.com/galaxyproject/galaxy/commit/14d6e34e010cafd98d8db2680c4c… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Rename from_html to from_json Commit: 40c9e1af255b548c35a9d98ac4c196058d185541 https://github.com/galaxyproject/galaxy/commit/40c9e1af255b548c35a9d98ac4c1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_select_parameters.py Log Message: ----------- Use value_to_basic and to_json when populating the tool model Commit: 773095d403929ad7f44561ff17f960f088f1b9ce https://github.com/galaxyproject/galaxy/commit/773095d403929ad7f44561ff17f9… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M test/unit/tools/test_data_parameters.py Log Message: ----------- Unify json representation for regular datasets and collections Commit: b1a9823a3c596a303973b8e1dbbd734a67c392ef https://github.com/galaxyproject/galaxy/commit/b1a9823a3c596a303973b8e1dbbd… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py Log Message: ----------- Remove RuntimeValue arrays Commit: 3c402a372338565bd4cf6056abc16da30c91a789 https://github.com/galaxyproject/galaxy/commit/3c402a372338565bd4cf6056abc1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py Log Message: ----------- Remove __collection_reduce__ Commit: 79a0972675a3594292c7e28e36639d67d49863ad https://github.com/galaxyproject/galaxy/commit/79a0972675a3594292c7e28e3663… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-12 (Sat, 12 Mar 2016) Changed paths: M lib/galaxy/tools/parameters/basic.py Log Message: ----------- Improve empty dataset check, handle from_json inconsistency Commit: ff0bcd392015d7b824b99b15b271c8b6f608b589 https://github.com/galaxyproject/galaxy/commit/ff0bcd392015d7b824b99b15b271… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-14 (Mon, 14 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/evaluation.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/workflow/modules.py M test/unit/tools/test_column_parameters.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_select_parameters.py Log Message: ----------- Merge pull request #1901 from guerler/fix_basic_000 Use shared value serialization for tool model Compare: https://github.com/galaxyproject/galaxy/compare/5d633ab5999b...ff0bcd392015

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[galaxyproject/galaxy] e61e59: Modify run.sh to add --restart option, for a more ...
by GitHub 12 Mar '16

12 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e61e596d88e4cc8f7cd41d2a2a678d5a3dffd72d https://github.com/galaxyproject/galaxy/commit/e61e596d88e4cc8f7cd41d2a2a67… Author: Remi Marenco <remi.marenco(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M run.sh Log Message: ----------- Modify run.sh to add --restart option, for a more consisten use of parameters Commit: 5d633ab5999bbb59fb217185f9ff524df3445166 https://github.com/galaxyproject/galaxy/commit/5d633ab5999bbb59fb217185f9ff… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-12 (Sat, 12 Mar 2016) Changed paths: M run.sh Log Message: ----------- Merge pull request #1914 from remimarenco/run_restart_modification Modify run.sh to add --restart option, for a more consistent use of pa… Compare: https://github.com/galaxyproject/galaxy/compare/957a8ff885dc...5d633ab5999b

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[galaxyproject/galaxy] 3476c7: Split the path on 'repos', so that toolsheds that ...
by GitHub 11 Mar '16

11 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3476c7f92848ff650bc9d148ad95712adf45c8ae https://github.com/galaxyproject/galaxy/commit/3476c7f92848ff650bc9d148ad95… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Split the path on 'repos', so that toolsheds that are on a subdirectory do not show errors when loading tools if there is actually no error. Commit: 957a8ff885dc0c20650971ada53d7b203dcd280f https://github.com/galaxyproject/galaxy/commit/957a8ff885dc0c20650971ada53d… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/galaxy/tools/toolbox/base.py Log Message: ----------- Merge pull request #1910 from mvdbeek/fix_not_an_error_1 do not assume toolshed to be on URL root Compare: https://github.com/galaxyproject/galaxy/compare/8423fe74dfc3...957a8ff885dc

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[galaxyproject/galaxy] b3e939: Replace get_tool_shed_repository_by_tool_shed_name...
by GitHub 11 Mar '16

11 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: b3e9398c3affa964fdc8cf090eb5c149f7a6bf47 https://github.com/galaxyproject/galaxy/commit/b3e9398c3affa964fdc8cf090eb5… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Replace get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision with get_repository_for_dependency_relationship Commit: d6e38c7d482eae65fc135cd65a13b7f215220cd5 https://github.com/galaxyproject/galaxy/commit/d6e38c7d482eae65fc135cd65a13… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- remove unused import Commit: 5a50a4691c11edb9366f2e0d3eeb68aaaabb9c80 https://github.com/galaxyproject/galaxy/commit/5a50a4691c11edb9366f2e0d3eeb… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py Log Message: ----------- Merge pull request #1909 from mvdbeek/backport_repository_for_dependency_relationship [16.01] Backport PR #1868 Compare: https://github.com/galaxyproject/galaxy/compare/3abd2c213ae5...5a50a4691c11

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[galaxyproject/galaxy] 50f108: Slight tweaks to our tabix usage. This fixes trac...
by GitHub 11 Mar '16

11 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 50f1089c72ff46397e525d4aa99dc80569081509 https://github.com/galaxyproject/galaxy/commit/50f1089c72ff46397e525d4aa99d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Slight tweaks to our tabix usage. This fixes trackster without more divergence in our version of pysam. Commit: c6f3e9b5b28268cba1ef8d7be5f1bed90b6ecc00 https://github.com/galaxyproject/galaxy/commit/c6f3e9b5b28268cba1ef8d7be5f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Slight cleanup, remove outdated comment regarding tabixfile.close() Commit: f0b7a34dd3ea5b3b10494c7e186fb10fda30441f https://github.com/galaxyproject/galaxy/commit/f0b7a34dd3ea5b3b10494c7e186f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Apply patch from Fabien Mareuil to resolve json serialization of Decimal error; for more see http://dev.list.galaxyproject.org/quota-api-error-td4669081.html Commit: a351c75687921bb8d2487577c5c4c0a64bee5e5f https://github.com/galaxyproject/galaxy/commit/a351c75687921bb8d2487577c5c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Extra documentation for @mvdbeek Commit: afb4e9c8f40da5331412c2a8f83ece814fb54b05 https://github.com/galaxyproject/galaxy/commit/afb4e9c8f40da5331412c2a8f83e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #1897 from dannon/pysam_compat [16.01] Slight tweaks to our tabix usage. Commit: 3abd2c213ae508bd3547d08729c96bbff4a5b740 https://github.com/galaxyproject/galaxy/commit/3abd2c213ae508bd3547d08729c9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Merge pull request #1898 from dannon/quota_api_fix_fabien [16.01] Quota API issue with serialization to JSON of Decimal Commit: 8423fe74dfc3b5effa70e771fd6a58df01b85d02 https://github.com/galaxyproject/galaxy/commit/8423fe74dfc3b5effa70e771fd6a… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Merge branch 'release_16.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/dd07156e1109...8423fe74dfc3

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[galaxyproject/galaxy] 824c22: Very basic tool error sentry reporting.
by GitHub 11 Mar '16

11 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 824c22942e5619859f37ddb0319ef367ea4231f1 https://github.com/galaxyproject/galaxy/commit/824c22942e5619859f37ddb0319e… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py Log Message: ----------- Very basic tool error sentry reporting. Commit: f46f1d58080a37e97d0add17dd95806af2987d4b https://github.com/galaxyproject/galaxy/commit/f46f1d58080a37e97d0add17dd95… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- Add tool version to title for grouping, and include path to tool config file. Commit: dd07156e1109f969a69be037c9122243bd4810d0 https://github.com/galaxyproject/galaxy/commit/dd07156e1109f969a69be037c912… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/app.py M lib/galaxy/jobs/__init__.py Log Message: ----------- Merge pull request #1900 from dannon/sentry_tool_errors Very basic tool error sentry reporting. Compare: https://github.com/galaxyproject/galaxy/compare/effdc314da3f...dd07156e1109

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[galaxyproject/galaxy] f0b7a3: Apply patch from Fabien Mareuil to resolve json se...
by GitHub 11 Mar '16

11 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: f0b7a34dd3ea5b3b10494c7e186fb10fda30441f https://github.com/galaxyproject/galaxy/commit/f0b7a34dd3ea5b3b10494c7e186f… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Apply patch from Fabien Mareuil to resolve json serialization of Decimal error; for more see http://dev.list.galaxyproject.org/quota-api-error-td4669081.html Commit: 3abd2c213ae508bd3547d08729c96bbff4a5b740 https://github.com/galaxyproject/galaxy/commit/3abd2c213ae508bd3547d08729c9… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/quotas.py Log Message: ----------- Merge pull request #1898 from dannon/quota_api_fix_fabien [16.01] Quota API issue with serialization to JSON of Decimal Compare: https://github.com/galaxyproject/galaxy/compare/afb4e9c8f40d...3abd2c213ae5

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[galaxyproject/galaxy] 50f108: Slight tweaks to our tabix usage. This fixes trac...
by GitHub 11 Mar '16

11 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 50f1089c72ff46397e525d4aa99dc80569081509 https://github.com/galaxyproject/galaxy/commit/50f1089c72ff46397e525d4aa99d… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Slight tweaks to our tabix usage. This fixes trackster without more divergence in our version of pysam. Commit: c6f3e9b5b28268cba1ef8d7be5f1bed90b6ecc00 https://github.com/galaxyproject/galaxy/commit/c6f3e9b5b28268cba1ef8d7be5f1… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Slight cleanup, remove outdated comment regarding tabixfile.close() Commit: a351c75687921bb8d2487577c5c4c0a64bee5e5f https://github.com/galaxyproject/galaxy/commit/a351c75687921bb8d2487577c5c4… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Extra documentation for @mvdbeek Commit: afb4e9c8f40da5331412c2a8f83ece814fb54b05 https://github.com/galaxyproject/galaxy/commit/afb4e9c8f40da5331412c2a8f83e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/visualization/data_providers/genome.py Log Message: ----------- Merge pull request #1897 from dannon/pysam_compat [16.01] Slight tweaks to our tabix usage. Compare: https://github.com/galaxyproject/galaxy/compare/0c34d5bd3ff4...afb4e9c8f40d

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[galaxyproject/usegalaxy-playbook] e8e310: Updated slide rotation.
by GitHub 10 Mar '16

10 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: e8e31070269b56b05c88d61174d4e411dca1a9c5 https://github.com/galaxyproject/usegalaxy-playbook/commit/e8e31070269b56b0… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: A files/galaxy/common/static/welcome_img/GCC2016OralAbstracts.png A files/galaxy/common/static/welcome_img/GCC2016ScholarshipsInternational.png A files/galaxy/common/static/welcome_img/RDF2GraphGalaxy.png M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Updated slide rotation. Dropped PIA server; added RDF2Graph server. Added 2 GCC2016 deadline slides

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[galaxyproject/galaxy] 3f15d5: UI, histories: rework update system to check conte...
by GitHub 10 Mar '16

10 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3f15d5af213d4ba59e75f51c11b1aef4ed101428 https://github.com/galaxyproject/galaxy/commit/3f15d5af213d4ba59e75f51c11b1… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- UI, histories: rework update system to check contents based on update times of contents and only stop checking when history has no more running jobs Commit: 7855e0009d21dad14b998bae974d0978ff43c6c9 https://github.com/galaxyproject/galaxy/commit/7855e0009d21dad14b998bae974d… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-02-24 (Wed, 24 Feb 2016) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/layout/masthead.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/scratchbook.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-section.js M 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scripts/api/import_library_dataset_to_history.py M scripts/api/import_workflows_from_installed_tool_shed_repository.py M scripts/api/install_tool_shed_repositories.py M scripts/api/library_create_folder.py M scripts/api/library_create_library.py M scripts/api/library_upload_dir.py M scripts/api/library_upload_from_import_dir.py M scripts/api/load_data_with_metadata.py M scripts/api/repair_tool_shed_repository.py M scripts/api/request_type_create_from_xml.py M scripts/api/requests_update_state.py M scripts/api/reset_metadata_on_installed_repositories.py M scripts/api/sample_dataset_update_status.py M scripts/api/sample_update_state.py M scripts/api/search.py M scripts/api/sequencer_configuration_create.py M scripts/api/update.py M scripts/api/upload_to_history.py M scripts/api/workflow_delete.py M scripts/api/workflow_execute.py M scripts/api/workflow_execute_parameters.py M scripts/api/workflow_import.py M scripts/api/workflow_import_from_file_rpark.py M scripts/check_galaxy.py M scripts/cleanup_datasets/cleanup_datasets.py M scripts/cleanup_datasets/pgcleanup.py M scripts/cleanup_datasets/update_metadata.py M scripts/create_db.py M scripts/data_libraries/build_lucene_index.py M scripts/data_libraries/build_whoosh_index.py M scripts/db_shell.py M scripts/edam_mapping.py M scripts/extract_dataset_part.py M scripts/functional_tests.py M scripts/galaxy-main M scripts/get_platforms.py M scripts/helper.py M scripts/loc_files/create_all_fasta_loc.py M scripts/manage_db.py M scripts/manage_tools.py M scripts/microbes/BeautifulSoup.py M scripts/microbes/create_bacteria_loc_file.py M scripts/microbes/create_bacteria_table.py M scripts/microbes/create_nib_seq_loc_file.py M scripts/microbes/get_builds_lengths.py M scripts/microbes/harvest_bacteria.py M scripts/microbes/ncbi_to_ucsc.py M scripts/microbes/util.py M scripts/migrate_tools/migrate_tools.py M scripts/others/incorrect_gops_jobs.py M scripts/others/incorrect_gops_join_jobs.py M scripts/paster.py A scripts/patch.sh M scripts/set_dataset_sizes.py M scripts/set_user_disk_usage.py M scripts/tool_shed/build_ts_whoosh_index.py M scripts/tool_shed/check_download_urls.py M scripts/tool_shed/migrate_tools_to_repositories.py M scripts/tools/maf/check_loc_file.py M scripts/tools/re_escape_output.py M scripts/transfer.py M scripts/update_shed_config_path.py M static/maps/mvc/workflow/workflow-view.js.map M static/maps/onload.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/workflow/workflow-view.js M static/scripts/onload.js M static/style/blue/base.css R templates/admin/requests/select_datasets_to_transfer.mako M templates/admin/tool_shed_repository/common.mako M templates/webapps/galaxy/requests/common/common.mako M templates/webapps/galaxy/requests/common/view_request_history.mako M templates/webapps/galaxy/requests/common/view_sample_datasets.mako M templates/webapps/galaxy/workflow/run.mako M templates/webapps/tool_shed/repository/common.mako M test/api/test_tools.py M test/api/test_workflows.py M test/api/test_workflows_from_yaml.py M test/docker/base/Dockerfile M test/docker/base/run_test_wrapper.sh A test/functional/tools/empty_output.xml M test/functional/tools/output_format.xml M test/functional/tools/samples_tool_conf.xml A test/functional/tools/strict_shell.xml A test/functional/tools/strict_shell_default_off.xml A test/functional/tools/validation_empty_dataset.xml M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py M test/unit/jobs/test_command_factory.py M test/unit/jobs/test_job_wrapper.py M test/unit/test_objectstore.py M test/unit/tools/test_evaluation.py A test/unit/tools/test_history_imp_exp.py M test/unit/tools/test_parsing.py M test/unit/tools_support.py M test/unit/unittest_utils/galaxy_mock.py M test/unit/workflows/test_render.py M tox.ini Log Message: ----------- (merge conflicts) Commit: 8078306d9af4ce4ebff5b85f20290ee11c98177a https://github.com/galaxyproject/galaxy/commit/8078306d9af4ce4ebff5b85f2029… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-04 (Fri, 04 Mar 2016) Changed paths: M lib/galaxy/managers/histories.py Log Message: ----------- History manager: remove unused import Commit: c15e5db2eca3e177febe2da43bfa41b9bcbd4455 https://github.com/galaxyproject/galaxy/commit/c15e5db2eca3e177febe2da43bfa… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-07 (Mon, 07 Mar 2016) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tours.js M config/tool_conf.xml.main M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/tabular.py M lib/galaxy/external_services/result_handlers/basic.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/actions/post.py M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py M lib/galaxy/jobs/transfer_manager.py M lib/galaxy/managers/context.py M lib/galaxy/model/metadata.py M lib/galaxy/model/search.py M lib/galaxy/queue_worker.py M lib/galaxy/tools/actions/__init__.py M lib/galaxy/tools/actions/metadata.py M lib/galaxy/tools/actions/upload_common.py M lib/galaxy/tools/imp_exp/__init__.py M lib/galaxy/tools/imp_exp/export_history.py M lib/galaxy/tools/parameters/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/parameters/validation.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/dbkeys.py M lib/galaxy/util/json.py M lib/galaxy/visualization/data_providers/basic.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/visualization/genomes.py M lib/galaxy/visualization/plugins/resource_parser.py M lib/galaxy/web/framework/base.py M lib/galaxy/web/framework/decorators.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/lda_datasets.py M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py M lib/galaxy/webapps/galaxy/api/tools.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py M lib/galaxy/webapps/galaxy/controllers/data_manager.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/library_common.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/webapps/galaxy/controllers/user.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/tool_shed/controllers/repository.py M lib/galaxy/workflow/modules.py M lib/tool_shed/galaxy_install/repair_repository_manager.py M lib/tool_shed/galaxy_install/update_repository_manager.py M lib/tool_shed/grids/repository_grids.py M lib/tool_shed/util/readme_util.py M lib/tool_shed/util/shed_util_common.py M lib/tool_shed/util/workflow_util.py M manage_tools.sh M run_reports.sh M run_tool_shed.sh M scripts/check_python.py M scripts/functional_tests.py M scripts/transfer.py M static/maps/layout/menu.js.map M static/maps/mvc/tours.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/layout/menu.js M static/scripts/mvc/tours.js M templates/webapps/tool_shed/repository/view_repository.mako M test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py M test/tool_shed/base/twilltestcase.py M tools/data_source/upload.py Log Message: ----------- (manually merge conflicts) Commit: d9fc71510a4ce1c7829457f518f672859d372ed9 https://github.com/galaxyproject/galaxy/commit/d9fc71510a4ce1c7829457f518f6… Author: carlfeberhard <carlfeberhard(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js M client/galaxy/scripts/mvc/workflow/workflow-canvas.js M lib/galaxy/managers/workflows.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/web/framework/base.py M lib/galaxy/webapps/galaxy/controllers/root.py M lib/galaxy/workflow/modules.py M lib/galaxy/workflow/run_request.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/util/workflow_util.py M static/maps/mvc/dataset/dataset-li-edit.js.map M static/maps/mvc/workflow/workflow-canvas.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/dataset/dataset-li-edit.js M static/scripts/mvc/workflow/workflow-canvas.js M templates/webapps/galaxy/workflow/editor.mako M templates/webapps/galaxy/workflow/run.mako M test/unit/workflows/test_modules.py Log Message: ----------- (merge conflicts) Commit: 4fd5df6d58ac4ddab59006c5251bdf3ef723de68 https://github.com/galaxyproject/galaxy/commit/4fd5df6d58ac4ddab59006c5251b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Rebuild client, bundles had unresolved conflicts committed previously. Commit: effdc314da3f05908eee4770354b457505bfffb4 https://github.com/galaxyproject/galaxy/commit/effdc314da3f05908eee4770354b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M client/galaxy/scripts/mvc/history/history-contents.js M client/galaxy/scripts/mvc/history/history-model.js M client/galaxy/scripts/mvc/history/history-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M lib/galaxy/managers/histories.py M lib/galaxy/managers/history_contents.py M lib/galaxy/model/__init__.py M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js M static/scripts/bundled/libs.bundled.js.map M static/scripts/bundled/login.bundled.js M static/scripts/bundled/login.bundled.js.map M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-view.js M static/scripts/mvc/history/multi-panel.js Log Message: ----------- Merge branch 'history.updating' into dev Compare: https://github.com/galaxyproject/galaxy/compare/6b96f7d5abce...effdc314da3f

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[galaxyproject/galaxy] f91796: Swap unpinned requirements.txt and conda-environme...
by GitHub 10 Mar '16

10 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: f91796d7a652d93d2fbcaafc16a7b0654ce4af2e https://github.com/galaxyproject/galaxy/commit/f91796d7a652d93d2fbcaafc16a7… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Swap unpinned requirements.txt and conda-environment.txt svgfig->svgwrite Commit: a7b1ce76700b99de782fd3c031cc456b4090599f https://github.com/galaxyproject/galaxy/commit/a7b1ce76700b99de782fd3c031cc… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M doc/source/admin/framework_dependencies.rst Log Message: ----------- Update doc Commit: 6b96f7d5abce39ccb58c947b81daaeb5744bab2b https://github.com/galaxyproject/galaxy/commit/6b96f7d5abce39ccb58c947b81da… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M doc/source/admin/framework_dependencies.rst M lib/galaxy/dependencies/conda-environment.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1896 from dannon/svgwrite_svgfig_deps svgfig->svgwrite in unpinned requirements Compare: https://github.com/galaxyproject/galaxy/compare/8311b7233f15...6b96f7d5abce

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[galaxyproject/usegalaxy-playbook] 4c874c: Update galaxyprojectdotorg.galaxy role
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 4c874c3cdf1cbf6e1a3d687cafc5ee324dc7402d https://github.com/galaxyproject/usegalaxy-playbook/commit/4c874c3cdf1cbf6e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M roles/galaxyprojectdotorg.galaxy/README.md M roles/galaxyprojectdotorg.galaxy/defaults/main.yml M roles/galaxyprojectdotorg.galaxy/meta/.galaxy_install_info M roles/galaxyprojectdotorg.galaxy/tasks/dependencies.yml M roles/galaxyprojectdotorg.galaxy/tasks/main.yml Log Message: ----------- Update galaxyprojectdotorg.galaxy role

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[galaxyproject/ansible-galaxy]
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/tags/0.6.3 Home: https://github.com/galaxyproject/ansible-galaxy

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[galaxyproject/ansible-galaxy] e2393a: Use pinned-requirements.txt when fetching.
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: e2393aff87eb91dd283d09723a6eba2ea95780a4 https://github.com/galaxyproject/ansible-galaxy/commit/e2393aff87eb91dd283d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M README.md M defaults/main.yml M tasks/dependencies.yml Log Message: ----------- Use pinned-requirements.txt when fetching.

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[galaxyproject/usegalaxy-playbook] aa43ac: Update Main
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: aa43ac5e18e08358cb98ffa20cd643ad85845434 https://github.com/galaxyproject/usegalaxy-playbook/commit/aa43ac5e18e08358… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main Commit: c24f864205e9b58998befe56ff245eacac0ed5d7 https://github.com/galaxyproject/usegalaxy-playbook/commit/c24f864205e9b589… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M production/files/interactive_environments/plugins/.ansible_ie_role_current_version M production/files/interactive_environments/proxy/.ansible_ie_role_current_version Log Message: ----------- Update IE versions Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/14427de5dd47...…

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[galaxyproject/galaxy] 9b251e: Tones down the warning message about tool changes
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9b251e567b0a1d5c7600d6aae7df7f22c7831700 https://github.com/galaxyproject/galaxy/commit/9b251e567b0a1d5c7600d6aae7df… Author: Brad Langhorst <brad(a)langhorst.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Tones down the warning message about tool changes This looked like an error to people here. I think this proposed language is a bit softer, but still conveys the message that users can proceed but should review the changes first to make sure their results will not be affected. Commit: 079d645bebad8b531d926f08703c5a2ae180b9d5 https://github.com/galaxyproject/galaxy/commit/079d645bebad8b531d926f08703c… Author: Brad Langhorst <brad(a)langhorst.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- typo fix Commit: 7955a2b769d02e57ed609b636621cd76d27bc3a8 https://github.com/galaxyproject/galaxy/commit/7955a2b769d02e57ed609b636621… Author: Brad Langhorst <brad(a)langhorst.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Update run.mako Commit: 8311b7233f15c04596322db57ca232e8f368d318 https://github.com/galaxyproject/galaxy/commit/8311b7233f15c04596322db57ca2… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M templates/webapps/galaxy/workflow/run.mako Log Message: ----------- Merge pull request #1893 from bwlang/patch-1 Tones down the warning message about tool changes Compare: https://github.com/galaxyproject/galaxy/compare/cd26a567e84b...8311b7233f15

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[galaxyproject/galaxy] 8d71c3: Change to sentry middleware to work with modern ra...
by GitHub 09 Mar '16

09 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8d71c3dc1b7ed1ad33f60af1f1fe71e4c7ece108 https://github.com/galaxyproject/galaxy/commit/8d71c3dc1b7ed1ad33f60af1f1fe… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Change to sentry middleware to work with modern raven clients. This allows us to upgrade raven and actually show the entire event_id to users on the guru meditation page. Commit: cd26a567e84bbe736d3dcfbcbe37da7070045823 https://github.com/galaxyproject/galaxy/commit/cd26a567e84bbe736d3dcfbcbe37… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-09 (Wed, 09 Mar 2016) Changed paths: M lib/galaxy/web/framework/middleware/sentry.py Log Message: ----------- Merge pull request #1895 from dannon/sentry_event_id Change to sentry middleware to work with modern raven clients. Compare: https://github.com/galaxyproject/galaxy/compare/36d85e81eecd...cd26a567e84b

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[galaxyproject/usegalaxy-playbook] 14427d: Mutable configs on Test + fix the Test config to r...
by GitHub 08 Mar '16

08 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 14427de5dd473ae9020b4ea2118e6f91c6f2d715 https://github.com/galaxyproject/usegalaxy-playbook/commit/14427de5dd473ae9… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml M stage/group_vars/galaxyservers.yml Log Message: ----------- Mutable configs on Test + fix the Test config to remove a duplication

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[galaxyproject/usegalaxy-playbook] 195454: Update Test
by GitHub 08 Mar '16

08 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 195454dc2362dee23e9170e2990cba5f875ef016 https://github.com/galaxyproject/usegalaxy-playbook/commit/195454dc2362dee2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

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[galaxyproject/infrastructure-playbook] 9e9077: Install sentry on galaxy06
by GitHub 08 Mar '16

08 Mar '16

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 9e9077c991fc7ec0b6ef5ab317d7262723a6a6b4 https://github.com/galaxyproject/infrastructure-playbook/commit/9e9077c991f… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M common_roles A roles/sentry/defaults/main.yml A roles/sentry/tasks/main.yml A roles/sentry/templates/redis.conf.j2 A roles/sentry/templates/sentry.conf.py.j2 A roles/sentry/templates/uwsgi.ini.j2 M taccenv/group_vars/statsservers.yml M taccenv/host_vars/galaxy06.tacc.utexas.edu.yml M taccenv/playbook.yml M taccenv/secret_group_vars/ssl.yml M taccenv/templates/nginx/sentry.j2 A taccenv/templates/supervisor/sentry.j2 Log Message: ----------- Install sentry on galaxy06

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