March 2016 - galaxy-commits - lists.galaxyproject.org

[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

1 0

[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

1 0

[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.

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[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

1 0

[galaxyproject/galaxy] 824c22: Very basic tool error sentry reporting.
by GitHub 10 Mar '16

10 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

1 0