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

[galaxyproject/galaxy] b7b04e: Fix tool downloads
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b7b04ee92033ca9a2e961e296f74378753ab0563 https://github.com/galaxyproject/galaxy/commit/b7b04ee92033ca9a2e961e296f74… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Fix tool downloads Commit: c7d1f009a163f8e74905c5c4ee5cc2e2288051c9 https://github.com/galaxyproject/galaxy/commit/c7d1f009a163f8e74905c5c4ee5c… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/tools/__init__.py Log Message: ----------- Merge pull request #1935 from guerler/fix_downloads_000 Fix tool downloads in tool form Compare: https://github.com/galaxyproject/galaxy/compare/cef58abb55e2...c7d1f009a163

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[galaxyproject/galaxy] 80562a: Fix API method broken in 6e13c3999.
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 80562acfe8979433620da5ad416705c7c845aad5 https://github.com/galaxyproject/galaxy/commit/80562acfe8979433620da5ad4167… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Fix API method broken in 6e13c3999. Commit: 381afd7576309409d788a6cf7cfe97f4f1421b04 https://github.com/galaxyproject/galaxy/commit/381afd7576309409d788a6cf7cfe… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Prevent server error if name or owner are missing. Commit: ad6edac562bd2fcfb0c49dc88bde692ced67ae02 https://github.com/galaxyproject/galaxy/commit/ad6edac562bd2fcfb0c49dc88bde… Author: Dave Bouvier <dave(a)bx.psu.edu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py Log Message: ----------- Also prevent server error when repository is not found. Commit: cef58abb55e261c05de97b9d99906cc60b6416ba https://github.com/galaxyproject/galaxy/commit/cef58abb55e261c05de97b9d9990… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/webapps/tool_shed/api/repositories.py M lib/galaxy/webapps/tool_shed/model/__init__.py Log Message: ----------- Merge pull request #1943 from davebx/ts_api_bug Fix API method broken in 6e13c3999. Compare: https://github.com/galaxyproject/galaxy/compare/89b25edc313d...cef58abb55e2

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[galaxyproject/galaxy] 13f05d: Allow testing element counts in tool output collec...
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 13f05d2d79a01e0fdde34eb8f7a2a02917a7c607 https://github.com/galaxyproject/galaxy/commit/13f05d2d79a01e0fdde34eb8f7a2… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/tools/parser/interface.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml Log Message: ----------- Allow testing element counts in tool output collections. Commit: 89b25edc313d4dd411af4f94d8dc830f2b37b945 https://github.com/galaxyproject/galaxy/commit/89b25edc313d4dd411af4f94d8dc… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M lib/galaxy/tools/parser/interface.py M test/functional/test_toolbox.py M test/functional/tools/collection_creates_list.xml Log Message: ----------- Merge pull request #1942 from jmchilton/element_count_test Allow testing element counts in tool output collections. Compare: https://github.com/galaxyproject/galaxy/compare/7fad23614b2a...89b25edc313d

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[galaxyproject/galaxy] 3e5aa6: More debugging for transiently failing tool test.
by GitHub 17 Mar '16

17 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3e5aa68ccfd1dcb117cc4131134cbe0c410a21cb https://github.com/galaxyproject/galaxy/commit/3e5aa68ccfd1dcb117cc4131134c… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M test/base/twilltestcase.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py Log Message: ----------- More debugging for transiently failing tool test. Commit: 7fad23614b2aaf4de1de4dc07829394ecf1d00c3 https://github.com/galaxyproject/galaxy/commit/7fad23614b2aaf4de1de4dc07829… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-17 (Thu, 17 Mar 2016) Changed paths: M test/base/twilltestcase.py M test/tool_shed/base/twilltestcase.py M test/tool_shed/functional/test_0490_export_import_repositories.py M test/tool_shed/functional/test_0500_export_repository_simple_dependency.py Log Message: ----------- Merge pull request #1939 from jmchilton/transient_ts_test More debugging for transiently failing tool shed test. Compare: https://github.com/galaxyproject/galaxy/compare/29b6d545cf22...7fad23614b2a

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[galaxyproject/galaxy] 46728c: Add bam.iobio as a display application.
by GitHub 16 Mar '16

16 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 46728c5728bde2f5587578b1ddd430c4d78757df https://github.com/galaxyproject/galaxy/commit/46728c5728bde2f5587578b1ddd4… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/iobio/bam.xml M lib/galaxy/datatypes/display_applications/application.py A tool-data/bam_iobio.loc.sample Log Message: ----------- Add bam.iobio as a display application. Commit: 0c57453c96f1619a9891d1d659610c44fd12e698 https://github.com/galaxyproject/galaxy/commit/0c57453c96f1619a9891d1d65961… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Add vcf.iobio as a display application. Commit: 915993bbd8f82afef9b68f5d8820437a07f6f264 https://github.com/galaxyproject/galaxy/commit/915993bbd8f82afef9b68f5d8820… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: A display_applications/iobio/vcf.xml Log Message: ----------- Add display_applications/iobio/vcf.xml. Commit: e6bb45b29ab20ef64834ca6c2908ae72c44beed8 https://github.com/galaxyproject/galaxy/commit/e6bb45b29ab20ef64834ca6c2908… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M tool-data/vcf_iobio.loc.sample Log Message: ----------- typo Commit: 29b6d545cf229518840e29d7468d65e4221db95a https://github.com/galaxyproject/galaxy/commit/29b6d545cf229518840e29d7468d… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M config/datatypes_conf.xml.sample M config/tool_data_table_conf.xml.sample A display_applications/iobio/bam.xml A display_applications/iobio/vcf.xml M lib/galaxy/datatypes/display_applications/application.py A tool-data/bam_iobio.loc.sample A tool-data/vcf_iobio.loc.sample Log Message: ----------- Merge pull request #1926 from blankenberg/iobio-display Add iobio external display applications for BAM and VCF. Compare: https://github.com/galaxyproject/galaxy/compare/aae2006079a9...29b6d545cf22

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[galaxyproject/galaxy] 84865c: Retrieve authentification also for long urls from ...
by GitHub 16 Mar '16

16 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 84865c893e1c089eefed69aeb0300afa7419d500 https://github.com/galaxyproject/galaxy/commit/84865c893e1c089eefed69aeb030… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-11 (Fri, 11 Mar 2016) Changed paths: M lib/tool_shed/tool_shed_registry.py Log Message: ----------- Retrieve authentification also for long urls from shed_auth Commit: aae2006079a9e0e5fc744ae2026e6deaa7d1a2f3 https://github.com/galaxyproject/galaxy/commit/aae2006079a9e0e5fc744ae2026e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/tool_shed/tool_shed_registry.py Log Message: ----------- Merge pull request #1912 from mvdbeek/relax_password_manager_matching Retrieve authentification also for long urls Compare: https://github.com/galaxyproject/galaxy/compare/e86969b4cbe3...aae2006079a9

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[galaxyproject/galaxy] 497694: Fix icon sizes
by GitHub 16 Mar '16

16 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4976945ab0f4388f5b6ed6916bb7ef123c28c0e9 https://github.com/galaxyproject/galaxy/commit/4976945ab0f4388f5b6ed6916bb7… Author: guerler <aysam.guerler(a)gmail.com> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.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/tool/tool-form.js M static/style/blue/base.css Log Message: ----------- Fix icon sizes Commit: e86969b4cbe3fb22a13aca9fdc17fc668f862ceb https://github.com/galaxyproject/galaxy/commit/e86969b4cbe3fb22a13aca9fdc17… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form.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/tool/tool-form.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1934 from guerler/fix_icon_size_000 Fix icon sizes Compare: https://github.com/galaxyproject/galaxy/compare/46dc26eeda4c...e86969b4cbe3

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[galaxyproject/galaxy] 18a4ed: FTP directory not existing should be a warning, no...
by GitHub 16 Mar '16

16 Mar '16

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 18a4edc1ca1bd491f644e6ee8ca011950cb15797 https://github.com/galaxyproject/galaxy/commit/18a4edc1ca1bd491f644e6ee8ca0… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- FTP directory not existing should be a warning, not an exception Commit: 5c45746e4203d22edfa03c10de6cbf830ff3bf5f https://github.com/galaxyproject/galaxy/commit/5c45746e4203d22edfa03c10de6c… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/galaxy/model/custom_types.py Log Message: ----------- Metadata above max size should be a warning. Commit: 46dc26eeda4c6bb98a951536da1ed9cf4c7e8f75 https://github.com/galaxyproject/galaxy/commit/46dc26eeda4c6bb98a951536da1e… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2016-03-16 (Wed, 16 Mar 2016) Changed paths: M lib/galaxy/model/custom_types.py M lib/galaxy/webapps/galaxy/api/remote_files.py Log Message: ----------- Merge pull request #1936 from mvdbeek/more_warnings_less_errors More warnings, less errors Compare: https://github.com/galaxyproject/galaxy/compare/9a0f971596a3...46dc26eeda4c

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[galaxyproject/galaxy] 29c78e: Fix virtualenv broken with #1847.
by GitHub 15 Mar '16

15 Mar '16

Branch: refs/heads/release_16.01 Home: https://github.com/galaxyproject/galaxy Commit: 29c78e984e52ac08b1b36a03e39b65c6edbe6200 https://github.com/galaxyproject/galaxy/commit/29c78e984e52ac08b1b36a03e39b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix virtualenv broken with #1847. Commit: 5824bc04af9270afbebcb2c8f9b6b3bea371b788 https://github.com/galaxyproject/galaxy/commit/5824bc04af9270afbebcb2c8f9b6… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-08 (Tue, 08 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Fix duplicate print statement reported by @dannon... https://github.com/galaxyproject/galaxy/pull/1890#issuecomment-193873380 Commit: 438661e8945c1bb317f75dabe3db429ea779255d https://github.com/galaxyproject/galaxy/commit/438661e8945c1bb317f75dabe3db… Author: John Chilton <jmchilton(a)gmail.com> Date: 2016-03-10 (Thu, 10 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Another fix for virtualenv fixes. Commit: 00a7c3af057c0689a53748802740bc2002df375c https://github.com/galaxyproject/galaxy/commit/00a7c3af057c0689a53748802740… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2016-03-15 (Tue, 15 Mar 2016) Changed paths: M run_reports.sh M run_tool_shed.sh Log Message: ----------- Merge pull request #1890 from jmchilton/fix_virtualenvs [16.01] Fix virtual env handling broken with #1847. Compare: https://github.com/galaxyproject/galaxy/compare/9a343efe8b7d...00a7c3af057c

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[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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