galaxy-commits June 2017

galaxy-commits@lists.galaxyproject.org

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[galaxyproject/infrastructure-playbook] 6c5f03: Add training site
by GitHub 29 Jun '17

29 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6c5f035ab26faaa628d3c3950ba9878acd4a41de https://github.com/galaxyproject/infrastructure-playbook/commit/6c5f035ab26… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-29 (Thu, 29 Jun 2017) Changed paths: M galaxyenv/host_vars/chouffe.galaxyproject.org.yml A galaxyenv/templates/nginx/training.j2 Log Message: ----------- Add training site

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[galaxyproject/galaxy] 7c86c5: refactors tag manager to use only what it needs…
by GitHub 28 Jun '17

28 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7c86c5480bc03db4897e64da1abd4c41ea6056c3 https://github.com/galaxyproject/galaxy/commit/7c86c5480bc03db4897e64da1abd… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M lib/tool_shed/galaxy_install/install_manager.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- refactors tag manager to use only what it needs… an sql_alchemy session, not the full app. This makes it possible to use the tag manager from the model. Commit: 49ccf2f49c032ec7198db3b053ec53ce3b02a694 https://github.com/galaxyproject/galaxy/commit/49ccf2f49c032ec7198db3b053ec… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/managers/tags.py Log Message: ----------- Should address too much indentation flake issue Commit: 8f416951bf9855497b2b0ea1a1d17f3b762c0518 https://github.com/galaxyproject/galaxy/commit/8f416951bf9855497b2b0ea1a1d1… Author: Brad Langhorst <langhorst(a)neb.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M lib/tool_shed/galaxy_install/install_manager.py Log Message: ----------- TagManager in toolshed is not related To GalaxyTagManager Fixes toolshed failing test Commit: 816912998115158a631f1d6114438c42f1f6ee2e https://github.com/galaxyproject/galaxy/commit/816912998115158a631f1d611443… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M lib/galaxy/app.py M lib/galaxy/managers/collections.py M lib/galaxy/managers/tags.py M lib/galaxy/model/__init__.py M lib/galaxy/web/base/controller.py M test/unit/unittest_utils/galaxy_mock.py Log Message: ----------- Merge pull request #4253 from bwlang/refactor_tag_manager refactors tag manager to use only what it needs… Compare: https://github.com/galaxyproject/galaxy/compare/dd0336e7d218...816912998115

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[galaxyproject/galaxy] aa70d3: Initial version
by GitHub 28 Jun '17

28 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: aa70d3da4e970d3af62716ffa9d8115ac7a7b80c https://github.com/galaxyproject/galaxy/commit/aa70d3da4e970d3af62716ffa9d8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: A SECURITY_POLICY.md Log Message: ----------- Initial version Commit: 21c066b3be2d0a8d112b0d3a7f7602aa1218650a https://github.com/galaxyproject/galaxy/commit/21c066b3be2d0a8d112b0d3a7f76… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M SECURITY_POLICY.md Log Message: ----------- Updates from @nsoranzo and @yhoogstrate Commit: 789e48f51e0b7d280d605ace70c6c1d365a4aa03 https://github.com/galaxyproject/galaxy/commit/789e48f51e0b7d280d605ace70c6… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- Link to secpol Commit: 64047040ceec6e5ec7597568cd9b1980a70b4662 https://github.com/galaxyproject/galaxy/commit/64047040ceec6e5ec7597568cd9b… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M SECURITY_POLICY.md Log Message: ----------- More rewordings Commit: 52740f68e181a30214291d5ee14c1b650b1aebc7 https://github.com/galaxyproject/galaxy/commit/52740f68e181a30214291d5ee14c… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M SECURITY_POLICY.md Log Message: ----------- Meh, I'm no good at this bit Commit: 12460ab86adeca5f3890d99fad9dbad0ca70cb7f https://github.com/galaxyproject/galaxy/commit/12460ab86adeca5f3890d99fad9d… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M SECURITY_POLICY.md Log Message: ----------- Small enhancements to SECURITY_POLICY.md Commit: 0730bf8adbf0aee745ff0312118acd1dccc97565 https://github.com/galaxyproject/galaxy/commit/0730bf8adbf0aee745ff0312118a… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M CONTRIBUTING.md Log Message: ----------- Remove any Commit: 6ad40726521b1dd4a024e831eae8c3d044c38b8a https://github.com/galaxyproject/galaxy/commit/6ad40726521b1dd4a024e831eae8… Author: Eric Rasche <rasche.eric(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M SECURITY_POLICY.md Log Message: ----------- Merge pull request #18 from nsoranzo/patch-1 Small enhancements to SECURITY_POLICY.md Commit: 93e5cd778f0c750f565b6f8901240533fe1e24ce https://github.com/galaxyproject/galaxy/commit/93e5cd778f0c750f565b6f890124… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M SECURITY_POLICY.md Log Message: ----------- Address @martenson's comments Commit: 66b9086f218f1585b9f2a080659e0507223711e9 https://github.com/galaxyproject/galaxy/commit/66b9086f218f1585b9f2a080659e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-05-16 (Tue, 16 May 2017) Changed paths: M SECURITY_POLICY.md Log Message: ----------- Add @jmchilton's comments Commit: f6f49bd020bad6f6f985b8782e2d0e46084ca1b4 https://github.com/galaxyproject/galaxy/commit/f6f49bd020bad6f6f985b8782e2d… Author: E Rasche <hxr(a)hx42.org> Date: 2017-05-24 (Wed, 24 May 2017) Changed paths: M doc/source/project/organization.rst Log Message: ----------- Security policies will fall under procedures Commit: dd0336e7d218ad72efc14052ff117551f9f654fd https://github.com/galaxyproject/galaxy/commit/dd0336e7d218ad72efc14052ff11… Author: Anton Nekrutenko <anekrut(a)gmail.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M CONTRIBUTING.md A SECURITY_POLICY.md M doc/source/project/organization.rst Log Message: ----------- Merge pull request #4113 from erasche/security-policy [PROCEDURES] Security policy Compare: https://github.com/galaxyproject/galaxy/compare/40cd2df06b05...dd0336e7d218

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[galaxyproject/galaxy] 9c10b6: For file sniffing, allow get_headers() to skip com...
by GitHub 28 Jun '17

28 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 9c10b6ce5de83494eb4ac6ad66d85b780cb5f4b5 https://github.com/galaxyproject/galaxy/commit/9c10b6ce5de83494eb4ac6ad66d8… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- For file sniffing, allow get_headers() to skip comment lines, which should prevent at least some instances of #3148. Commit: 3bb3ecb09bb0ac77668d08cb1d5ecc0b7d61fa29 https://github.com/galaxyproject/galaxy/commit/3bb3ecb09bb0ac77668d08cb1d5e… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/datatypes/sniff.py Log Message: ----------- Typo Commit: e6278a778d3e2b1e02c6cba49516a9f0ebdf5e5b https://github.com/galaxyproject/galaxy/commit/e6278a778d3e2b1e02c6cba49516… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Remove camel case Commit: e5e83833d13d54b695952d73279b011c3b996af8 https://github.com/galaxyproject/galaxy/commit/e5e83833d13d54b695952d73279b… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Style and ignore '' comment_designators Commit: 40cd2df06b058bad1c04281a134773a58631c60f https://github.com/galaxyproject/galaxy/commit/40cd2df06b058bad1c04281a1347… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M lib/galaxy/datatypes/interval.py M lib/galaxy/datatypes/sniff.py Log Message: ----------- Merge pull request #4239 from dpryan79/sniffSkipComments Enable skipping comment lines while sniffing files Compare: https://github.com/galaxyproject/galaxy/compare/6cd026bc7b32...40cd2df06b05

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[galaxyproject/galaxy] 694d8c: Sniff FastqSanger before Fastq, in the former case...
by GitHub 28 Jun '17

28 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 694d8c85551013a894a491d4be9e5a46b72fb199 https://github.com/galaxyproject/galaxy/commit/694d8c85551013a894a491d4be9e… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py Log Message: ----------- Sniff FastqSanger before Fastq, in the former case checking the quality scores for compatibility Commit: 0a942d79a326c3b2cfb8d7cbee6a341e4600a77f https://github.com/galaxyproject/galaxy/commit/0a942d79a326c3b2cfb8d7cbee6a… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/sequence.py Log Message: ----------- Checking the quality lines will make fastqsanger checks rather more relevant. Commit: bc13a16f83d9d74774751fbe5c4d7d3b2b3c6ecc https://github.com/galaxyproject/galaxy/commit/bc13a16f83d9d74774751fbe5c4d… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py Log Message: ----------- Add the compressed datatypes to the sniffer lsit Commit: ab1127334f1c0e2d43c4fcccb9259c33fdaf235b https://github.com/galaxyproject/galaxy/commit/ab1127334f1c0e2d43c4fcccb925… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Remove debugging stuff, since everything works inside of docker Commit: 798b73eb688c5b7786fe2b9ffe69967ded3d7c63 https://github.com/galaxyproject/galaxy/commit/798b73eb688c5b7786fe2b9ffe69… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/datatypes/registry.py Log Message: ----------- Fix line reordering Commit: 8eaede31102b16f09abcbc8f0f06c6eab75d49bb https://github.com/galaxyproject/galaxy/commit/8eaede31102b16f09abcbc8f0f06… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Fix sequence.py unit test Commit: f3853a09562af8d7539740344433c4a8dc94aa36 https://github.com/galaxyproject/galaxy/commit/f3853a09562af8d7539740344433… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Test a non-fastqsanger file and ensure it doesn't pass the sniff test. Commit: 907bd53776eccec0e8d3fadfb69223dadcc48600 https://github.com/galaxyproject/galaxy/commit/907bd53776eccec0e8d3fadfb692… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Make the phred range stricter and more explicit. Commit: e21e9ec15fec5d3d1e47cd3c3001d9be24fbf12c https://github.com/galaxyproject/galaxy/commit/e21e9ec15fec5d3d1e47cd3c3001… Author: Devon Ryan <dpryan79(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M lib/galaxy/datatypes/sequence.py Log Message: ----------- Ugh, there were multiple places where the sniffing order was specified (binary formats are different). Commit: 6cd026bc7b32866437ca6e4e996e0cddeb40f837 https://github.com/galaxyproject/galaxy/commit/6cd026bc7b32866437ca6e4e996e… Author: Marius van den Beek <m.vandenbeek(a)gmail.com> Date: 2017-06-28 (Wed, 28 Jun 2017) Changed paths: M config/datatypes_conf.xml.sample M lib/galaxy/datatypes/registry.py M lib/galaxy/datatypes/sequence.py Log Message: ----------- Merge pull request #4237 from dpryan79/fastqSniffer_implement3571 Sniff fastqsanger and prefer it over fastq if the quality scores match Compare: https://github.com/galaxyproject/galaxy/compare/e98378160a46...6cd026bc7b32

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[galaxyproject/galaxy] fa80b4: Merge pull request #1 from galaxyproject/dev
by GitHub 27 Jun '17

27 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: fa80b4961182ab7391fdd99624652288669851d5 https://github.com/galaxyproject/galaxy/commit/fa80b4961182ab7391fdd9962465… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2017-01-23 (Mon, 23 Jan 2017) Changed paths: M .ci/flake8_blacklist.txt A .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper.sh A .ci/flake8_wrapper_docstrings.sh A .ci/jenkins/api/run_tests.sh A .ci/jenkins/framework/run_tests.sh A .ci/jenkins/integration/run_tests.sh A .ci/jenkins/selenium/Dockerfile A .ci/jenkins/selenium/docker-compose.yml A .ci/jenkins/selenium/galaxy.ini A .ci/jenkins/selenium/run_galaxy.bash A .ci/jenkins/selenium/run_tests.sh A .ci/jenkins/toolshed/run_tests.sh M .ci/py3_sources.txt A .ci/validate_test_tools.sh M .gitignore M .travis.yml M CONTRIBUTORS.md M LICENSE.txt M Makefile M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/history-panel.js M 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tools/stats/grouping.py M tools/stats/gsummary.py M tools/visualization/LAJ_code.py M tox.ini Log Message: ----------- Merge pull request #1 from galaxyproject/dev Merge from upstream Commit: 0db0d7b367c4435c44c3f47b512d128735a78ad0 https://github.com/galaxyproject/galaxy/commit/0db0d7b367c4435c44c3f47b512d… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2017-06-02 (Fri, 02 Jun 2017) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_docstrings_include_list.txt M .ci/flake8_lint_include_list.txt M .ci/flake8_wrapper_docstrings.sh M .ci/jenkins/selenium/run_tests.sh M .ci/py3_sources.txt M .gitignore M .travis.yml M CITATION M CONTRIBUTING.md M CONTRIBUTORS.md M Makefile M README.rst A client/galaxy/scripts/admin.toolshed.js A client/galaxy/scripts/apps/admin.js M client/galaxy/scripts/apps/analysis.js R client/galaxy/scripts/apps/history-panel.js M client/galaxy/scripts/apps/login.js A client/galaxy/scripts/apps/panels/admin-panel.js A 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test/shed_functional/functional/test_1090_repository_dependency_handling.py M test/shed_functional/functional/test_1150_datatype_converters.py M test/unit/managers/test_HDAManager.py M test/unit/managers/test_HistoryManager.py M test/unit/tools/test_conda_resolution.py M test/unit/tools/test_data_parameters.py M test/unit/tools/test_execution.py M test/unit/tools/test_tool_deps.py M test/unit/tools/test_toolbox.py M test/unit/tools/test_watcher.py M test/unit/tools/test_wrappers.py M test/unit/workflows/test_modules.py M test/unit/workflows/test_workflow_progress.py M tool-data/shared/ucsc/builds.txt.sample M tool-data/shared/ucsc/ucsc_build_sites.txt.sample M tools/evolution/add_scores.xml M tools/extract/extract_genomic_dna.xml M tools/filters/pasteWrapper.xml M tools/filters/trimmer.py M tools/filters/trimmer.xml M tools/maf/genebed_maf_to_fasta.xml M tools/maf/interval2maf.xml M tools/maf/interval2maf_pairwise.xml M tools/maf/interval_maf_to_merged_fasta.xml M tools/maf/macros.xml M tools/maf/maf_by_block_number.xml M tools/maf/maf_filter.xml M tools/maf/maf_limit_size.xml M tools/maf/maf_limit_to_species.xml M tools/maf/maf_reverse_complement.xml M tools/maf/maf_split_by_species.xml M tools/maf/maf_stats.xml M tools/maf/maf_thread_for_species.xml M tools/maf/maf_to_bed.xml M tools/maf/maf_to_fasta.xml M tools/maf/maf_to_interval.xml M tools/maf/vcf_to_maf_customtrack.xml M tools/metag_tools/shrimp_color_wrapper.xml M tools/metag_tools/shrimp_wrapper.xml M tools/next_gen_conversion/fastq_gen_conv.xml M tools/stats/aggregate_binned_scores_in_intervals.xml M tox.ini Log Message: ----------- Merge pull request #2 from galaxyproject/dev Merge from upstream #2 Commit: 7dab2aac26a59af1bdf2d6314edf625636987d2f https://github.com/galaxyproject/galaxy/commit/7dab2aac26a59af1bdf2d6314edf… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2017-06-20 (Tue, 20 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .gitignore M client/galaxy/scripts/apps/analysis.js M 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config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M doc/Makefile R doc/patch.py R doc/source/api/api.rst R doc/source/api/ts_api.rst M doc/source/lib/galaxy.actions.rst M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.auth.rst A doc/source/lib/galaxy.containers.rst M doc/source/lib/galaxy.dataset_collections.rst M doc/source/lib/galaxy.dataset_collections.types.rst M doc/source/lib/galaxy.datatypes.converters.rst M doc/source/lib/galaxy.datatypes.dataproviders.rst M doc/source/lib/galaxy.datatypes.display_applications.rst M doc/source/lib/galaxy.datatypes.rst M doc/source/lib/galaxy.datatypes.util.rst M doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst 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test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/config/trans_object.yaml M test/functional/webhooks/trans_object/helper/__init__.py M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge pull request #3 from galaxyproject/dev Merge from upstream Commit: b1477a8b87198e5e47ab508633d9999edf047dc3 https://github.com/galaxyproject/galaxy/commit/b1477a8b87198e5e47ab508633d9… Author: pvanheus <pvh(a)webbedfeet.co.za> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M .ci/py3_sources.txt M .gitignore M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/apps/panels/tool-panel.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/layout/page.js M client/galaxy/scripts/layout/panel.js M 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lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/parameters/basic.py M lib/galaxy/tools/wrappers.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/history.py M lib/galaxy/webapps/galaxy/controllers/visualization.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M static/maps/layout/menu.js.map M static/maps/layout/page.js.map M static/maps/layout/panel.js.map M static/maps/mvc/grid/grid-view.js.map A static/maps/mvc/history/history-list.js.map M static/maps/mvc/history/history-view-edit-current.js.map M static/maps/mvc/history/options-menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/user/user-preferences.js.map M static/maps/mvc/workflow/workflow-configure-menu.js.map M static/maps/mvc/workflow/workflow.js.map M static/maps/utils/utils.js.map M static/scripts/bundled/admin.bundled.js M static/scripts/bundled/admin.bundled.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/layout/menu.js M static/scripts/layout/page.js M static/scripts/layout/panel.js M static/scripts/mvc/grid/grid-view.js A static/scripts/mvc/history/history-list.js M static/scripts/mvc/history/history-view-edit-current.js M static/scripts/mvc/history/options-menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/user/user-preferences.js M static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/scripts/utils/utils.js M static/style/blue/base.css R templates/webapps/galaxy/history/grid.mako R templates/webapps/galaxy/history/grid_js.mako R templates/webapps/galaxy/visualization/list_published.mako R templates/webapps/galaxy/workflow/import.mako R templates/webapps/galaxy/workflow/list_published.mako R templates/webapps/galaxy/workflow/run.mako M test/functional/tools/sample_datatypes_conf.xml Log Message: ----------- Merge pull request #4 from galaxyproject/dev Merge just before GCC2017 Commit: e63ababa79ed79cce8f999199578005a18d27d5c https://github.com/galaxyproject/galaxy/commit/e63ababa79ed79cce8f999199578… Author: Peter van Heusden <pvh(a)sanbi.ac.za> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- add public-only filter for data libraries Commit: c41b2849998250af2abc4d4655c0d6aaee27fc77 https://github.com/galaxyproject/galaxy/commit/c41b2849998250af2abc4d4655c0… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map 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.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- adjust logic to match the include deleted checkbox also make client and set default user preference Commit: 6a43fad892d870caf7f9fa12adb4c532a16e56c9 https://github.com/galaxyproject/galaxy/commit/6a43fad892d870caf7f9fa12adb4… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js A test-data/5_Ig-like.gff M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml M tools/filters/wc_gnu.xml Log Message: ----------- Merge branch 'dev' into lib_exclude_restricted Conflicts: static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map Commit: e98378160a46c97979daec4f6e1183cd6214fe79 https://github.com/galaxyproject/galaxy/commit/e98378160a46c97979daec4f6e11… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M client/galaxy/scripts/galaxy.library.js M client/galaxy/scripts/mvc/library/library-librarylist-view.js M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js M static/maps/galaxy.library.js.map M static/maps/mvc/library/library-librarylist-view.js.map M static/maps/mvc/library/library-librarytoolbar-view.js.map M static/scripts/bundled/admin.bundled.js.map 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.map M static/scripts/galaxy.library.js M static/scripts/mvc/library/library-librarylist-view.js M static/scripts/mvc/library/library-librarytoolbar-view.js Log Message: ----------- Merge pull request #4232 from pvanheus/dev add public-only filter for data libraries Compare: https://github.com/galaxyproject/galaxy/compare/153b8d4dca04...e98378160a46

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[galaxyproject/usegalaxy-playbook] 067433: Add missing twobit data table to by-hand tool_data...
by GitHub 27 Jun '17

27 Jun '17

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 067433f547f67b848f2e4597274a379f06da04b2 https://github.com/galaxyproject/usegalaxy-playbook/commit/067433f547f67b84… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M files/galaxy/usegalaxy.org/config/tool_data_table_conf.xml Log Message: ----------- Add missing twobit data table to by-hand tool_data_table_conf.xml for Main

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[galaxyproject/galaxy] 4f3129: - get real user name from username and email
by GitHub 27 Jun '17

27 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4f31290113eb1d106b8f1cf894a854c6c310a004 https://github.com/galaxyproject/galaxy/commit/4f31290113eb1d106b8f1cf894a8… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-22 (Mon, 22 May 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- - get real user name from username and email - sudo calls with preserving PATH, LD_LIBRARY_PATH ... Commit: b07ebdaadaf3d5d4eb089988638f193821015494 https://github.com/galaxyproject/galaxy/commit/b07ebdaadaf3d5d4eb089988638f… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- - added path check to external chown script Commit: 6841faac692e8b12f7634a547e69ff8a14a9506e https://github.com/galaxyproject/galaxy/commit/6841faac692e8b12f7634a547e69… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- - removed my paths Commit: d25e552003216d0f986148a161223b010cdcaee8 https://github.com/galaxyproject/galaxy/commit/d25e552003216d0f986148a16122… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-23 (Tue, 23 May 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- - removed uneccessary import - added quotes to comment Commit: 3a16b36df8471d8c89f5ae04e82199adc3933adf https://github.com/galaxyproject/galaxy/commit/3a16b36df8471d8c89f5ae04e821… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-24 (Wed, 24 May 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- made determination of actual user configurable Commit: 5ee0d7ec0e8d6279be5cbad44d5d41f4d66b317f https://github.com/galaxyproject/galaxy/commit/5ee0d7ec0e8d6279be5cbad44d5d… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- moved sudo calls to galaxy.ini removed spaces Commit: 01cffa6151f6086c4b944d1146a380d4b0e437da https://github.com/galaxyproject/galaxy/commit/01cffa6151f6086c4b944d1146a3… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-05-26 (Fri, 26 May 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- imroved external_chown_script now uses Popen and checks return code Commit: 64f5e2e2fa286bc3cc4151c523d8d98bb4dcf3fe https://github.com/galaxyproject/galaxy/commit/64f5e2e2fa286bc3cc4151c523d8… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2017-06-12 (Mon, 12 Jun 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py M scripts/external_chown_script.py Log Message: ----------- Fix linting issues Commit: e197cadd98491d8341b3894f5663ea047b2972d2 https://github.com/galaxyproject/galaxy/commit/e197cadd98491d8341b3894f5663… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- fix typo Commit: 71cd8ddcc73744b9e45fc1708be9601f41250dd5 https://github.com/galaxyproject/galaxy/commit/71cd8ddcc73744b9e45fc1708be9… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/model/__init__.py Log Message: ----------- Add system_user_pwent function Commit: 32d7a30943048e43b2700f33c399b6e0ccf2255a https://github.com/galaxyproject/galaxy/commit/32d7a30943048e43b2700f33c399… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/tools/actions/upload_common.py Log Message: ----------- Add system_user_pwent function to upload and jobs Commit: 2ec805417c6a251319714178e5be088cc285ebc9 https://github.com/galaxyproject/galaxy/commit/2ec805417c6a251319714178e5be… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- Change paramter typo Commit: e81a2ac65454e0dd88d474210036d166c3055a5b https://github.com/galaxyproject/galaxy/commit/e81a2ac65454e0dd88d474210036… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- Fix removed duplication in external chown script Commit: c275d25be9873e259777506e46b6f7989213e172 https://github.com/galaxyproject/galaxy/commit/c275d25be9873e259777506e46b6… Author: rhpvorderman <r.h.p.vorderman(a)lumc.nl> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- Fix linting Commit: aa200fe46351eaa6f7ab30899cdf57bdaa2b069a https://github.com/galaxyproject/galaxy/commit/aa200fe46351eaa6f7ab30899cdf… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/__init__.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/upload_common.py M scripts/external_chown_script.py Log Message: ----------- implemented the changes requested by @mvdbeek: - check for external_chown_script == None - switched from string split to shlex.split - changed import order for pwd - stderr + exit -> just exit Commit: e8f44de501dec8b04864b574687d8098ea3bab1e https://github.com/galaxyproject/galaxy/commit/e8f44de501dec8b04864b574687d… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/__init__.py Log Message: ----------- bugfix missing colon Commit: ae1903d396584fe51bf77127b84ea7cf7b831fb6 https://github.com/galaxyproject/galaxy/commit/ae1903d396584fe51bf77127b84e… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/jobs/runners/drmaa.py Log Message: ----------- shlex.split also for external kill and run scripts Commit: 7fbd3f2bc229d60da22535b062465b1794e39335 https://github.com/galaxyproject/galaxy/commit/7fbd3f2bc229d60da22535b06246… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M scripts/external_chown_script.py Log Message: ----------- added missing empty line Commit: 074b90d55edc0a82115aac3adc5b189e7144c0b3 https://github.com/galaxyproject/galaxy/commit/074b90d55edc0a82115aac3adc5b… Author: bernt(a)informatik.uni-leipzig.de <bernt(a)informatik.uni-leipzig.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M lib/galaxy/model/__init__.py M scripts/external_chown_script.py Log Message: ----------- bug fixes - system_user_pwent: undefined return value when KeyError - external_chown_script: * typo * subprocess instead of os.subprocess Commit: f83871d0707dea0256a5f409f285eec16f7bcef7 https://github.com/galaxyproject/galaxy/commit/f83871d0707dea0256a5f409f285… Author: bernt(a)informatik.uni-leipzig.de <bernt(a)informatik.uni-leipzig.de> Date: 2017-06-13 (Tue, 13 Jun 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/jobs/runners/drmaa.py M scripts/drmaa_external_runner.py Log Message: ----------- moved assign_all_groups parameter to config Commit: 351adc6574dce1e0be8f3e079a84b77f46f045f6 https://github.com/galaxyproject/galaxy/commit/351adc6574dce1e0be8f3e079a84… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-06-14 (Wed, 14 Jun 2017) Changed paths: M .ci/flake8_lint_include_list.txt M CONTRIBUTORS.md M README.rst M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/collection/collection-view.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/form/form-input.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/hda-li.js M client/galaxy/scripts/mvc/history/hdca-li.js A client/galaxy/scripts/mvc/page/page-list.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/ui/ui-slider.js A client/galaxy/scripts/mvc/workflow/workflow-configure-menu.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M 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lib/galaxy/util/compression_utils.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/webapps/galaxy/api/history_contents.py M lib/galaxy/webapps/galaxy/api/workflows.py M lib/galaxy/webapps/galaxy/buildapp.py M lib/galaxy/webapps/galaxy/controllers/dataset.py M lib/galaxy/webapps/galaxy/controllers/page.py M lib/galaxy/webapps/galaxy/controllers/workflow.py M lib/tool_shed/galaxy_install/install_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/metadata/metadata_generator.py M scripts/bootstrap_history.py M static/maps/layout/menu.js.map M static/maps/mvc/collection/collection-view.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/form/form-input.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/grid/grid-view.js.map M static/maps/mvc/history/hda-li.js.map M static/maps/mvc/history/hdca-li.js.map A 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static/scripts/mvc/workflow/workflow-configure-menu.js M static/scripts/mvc/workflow/workflow.js M static/style/blue/base.css M static/welcome.html.sample M templates/grid_base.mako M templates/sharing_base.mako R templates/webapps/galaxy/dataset/grid.mako M templates/webapps/galaxy/page/editor.mako R templates/webapps/galaxy/page/index.mako R templates/webapps/galaxy/page/list_published.mako R templates/webapps/galaxy/workflow/configure_menu.mako M test/api/test_dataset_collections.py M test/base/populators.py A test/functional/tools/mulled_example_multi_versionless.xml M test/functional/tools/sample_datatypes_conf.xml M test/functional/tools/samples_tool_conf.xml M test/functional/webhooks/trans_object/config/trans_object.yaml M test/qunit/test-data/bootstrapped.js M test/qunit/tests/galaxy-app-base.js M test/qunit/tests/ui_tests.html M test/qunit/tests/ui_tests.js A test/unit/jobs/conditional_runners_job_conf.xml M test/unit/jobs/test_job_configuration.py M test/unit/tools/test_toolbox.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 57c112442d53dfff5cc9be9c775fd81eb7cae03d https://github.com/galaxyproject/galaxy/commit/57c112442d53dfff5cc9be9c775f… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-06-15 (Thu, 15 Jun 2017) Changed paths: M config/galaxy.ini.sample Log Message: ----------- fixed typos in galaxy.ini Commit: 698075c3d7fa5745cc437d36a9c0c48e3f0c6f9f https://github.com/galaxyproject/galaxy/commit/698075c3d7fa5745cc437d36a9c0… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M .gitignore M client/galaxy/scripts/layout/menu.js M client/galaxy/scripts/mvc/tool/tool-form-base.js M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/tool/tool-form.js M client/galaxy/scripts/mvc/webhooks.js M client/galaxy/scripts/onload.js M config/plugins/webhooks/demo/tool_list/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml A config/plugins/webhooks/demo/tour_generator/helper/__init__.py A config/plugins/webhooks/demo/tour_generator/static/script.js A config/plugins/webhooks/demo/tour_generator/static/styles.css M cron/updateucsc.sh.sample M lib/galaxy/tools/deps/container_resolvers/mulled.py M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/mulled/invfile.lua M lib/galaxy/tools/deps/mulled/mulled_build.py M lib/galaxy/tools/deps/mulled/mulled_build_files.py M lib/galaxy/tools/deps/mulled/mulled_build_tool.py M lib/galaxy/webapps/galaxy/api/webhooks.py M scripts/api/library_upload_dir.py M static/maps/layout/menu.js.map M static/maps/mvc/tool/tool-form-base.js.map M static/maps/mvc/tool/tool-form-composite.js.map M static/maps/mvc/tool/tool-form.js.map M static/maps/mvc/webhooks.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/layout/menu.js M static/scripts/mvc/tool/tool-form-base.js M static/scripts/mvc/tool/tool-form-composite.js M static/scripts/mvc/tool/tool-form.js M static/scripts/mvc/webhooks.js M static/scripts/onload.js M templates/js-app.mako M test/functional/webhooks/phdcomics/helper/__init__.py M test/functional/webhooks/trans_object/helper/__init__.py Log Message: ----------- Merge remote-tracking branch 'upstream/dev' into dev Commit: 153b8d4dca041f43d704cab052b1b733d74658c8 https://github.com/galaxyproject/galaxy/commit/153b8d4dca041f43d704cab052b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M config/galaxy.ini.sample M lib/galaxy/config.py M lib/galaxy/jobs/__init__.py M lib/galaxy/jobs/runners/drmaa.py M lib/galaxy/model/__init__.py M lib/galaxy/tools/actions/upload_common.py M scripts/drmaa_external_runner.py M scripts/external_chown_script.py Log Message: ----------- Merge pull request #4096 from bernt-matthias/dev get real user name from username and email (for submission as real user with drmaa) Compare: https://github.com/galaxyproject/galaxy/compare/a57b4c171525...153b8d4dca04

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[galaxyproject/galaxy] b32c1c: Check name export in legacy export section
by GitHub 27 Jun '17

27 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: b32c1cf1a3143804b0c4f12f6f7235a87801a74d https://github.com/galaxyproject/galaxy/commit/b32c1cf1a3143804b0c4f12f6f72… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-16 (Fri, 16 Jun 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Check name export in legacy export section Commit: f7ba7295102c9ce9969c634ee89e26f02c2801ea https://github.com/galaxyproject/galaxy/commit/f7ba7295102c9ce9969c634ee89e… Author: John Chilton <jmchilton(a)gmail.com> Date: 2017-06-19 (Mon, 19 Jun 2017) Changed paths: M lib/galaxy/managers/workflows.py Log Message: ----------- Merge pull request #4203 from guerler/fix_name_export [17.05] Check name type in legacy export section Commit: 268ee7f1b7e65dde514098e0779b80b7589d26b5 https://github.com/galaxyproject/galaxy/commit/268ee7f1b7e65dde514098e0779b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Improve resilience of tool url building Commit: 69e76f98fa90782c37a2697de0204e4ff7945f09 https://github.com/galaxyproject/galaxy/commit/69e76f98fa90782c37a2697de020… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Remove redundancy of tool_id parameter Commit: a498390bef74301816945551a9832f38747fd4fc https://github.com/galaxyproject/galaxy/commit/a498390bef74301816945551a983… Author: guerler <aysam.guerler(a)gmail.com> Date: 2017-06-21 (Wed, 21 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map Log Message: ----------- Fix basic version changes for reloaded tools Commit: 9dca211e2fe59eaad1f7b95c8d51608b2afa05af https://github.com/galaxyproject/galaxy/commit/9dca211e2fe59eaad1f7b95c8d51… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2017-06-22 (Thu, 22 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge pull request #4214 from guerler/revise_tool_url [17.05] Improve resilience of tool url building Commit: a57b4c171525c5380eed832d015f73df10e23fee https://github.com/galaxyproject/galaxy/commit/a57b4c171525c5380eed832d015f… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2017-06-27 (Tue, 27 Jun 2017) Changed paths: M client/galaxy/scripts/mvc/tool/tool-form-base.js M lib/galaxy/managers/workflows.py M static/maps/mvc/tool/tool-form-base.js.map M static/scripts/bundled/analysis.bundled.js M static/scripts/bundled/analysis.bundled.js.map M static/scripts/bundled/libs.bundled.js.map M static/scripts/mvc/tool/tool-form-base.js Log Message: ----------- Merge branch 'release_17.05' into dev Conflicts: static/maps/mvc/tool/tool-form-base.js.map static/scripts/bundled/analysis.bundled.js static/scripts/bundled/analysis.bundled.js.map static/scripts/bundled/libs.bundled.js.map static/scripts/mvc/tool/tool-form-base.js Compare: https://github.com/galaxyproject/galaxy/compare/46dbf8d10c6d...a57b4c171525

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[galaxyproject/galaxy] cb40b0: Ignore blank lines and comments in GFF files
by GitHub 26 Jun '17

26 Jun '17

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: cb40b01db8a29e2662610ce3cec5bf104c939ba8 https://github.com/galaxyproject/galaxy/commit/cb40b01db8a29e2662610ce3cec5… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Ignore blank lines and comments in GFF files Previously would wrongly issue warnings about valid # lines. Closes #3067 Commit: c87e0eedb79247240875a411aec0799e3e2460b2 https://github.com/galaxyproject/galaxy/commit/c87e0eedb79247240875a411aec0… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: A test-data/5_Ig-like.gff M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml Log Message: ----------- Cope with GFF3 as well as legacy GFF. In GFF3 have key=value rather than space separated as in legacy GFF and GTF format. Closes #3068. Commit: 005f3d9f9837d91468bd8f253d2752e51885de10 https://github.com/galaxyproject/galaxy/commit/005f3d9f9837d91468bd8f253d27… Author: peterjc <p.j.a.cock(a)googlemail.com> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: M tools/filters/gff/gff_filter_by_attribute.py Log Message: ----------- Defensive code in case standard GFF fields missing Commit: 46dbf8d10c6d229a53566e799b36aa34c1a83c7c https://github.com/galaxyproject/galaxy/commit/46dbf8d10c6d229a53566e799b36… Author: Björn Grüning <bjoern(a)gruenings.eu> Date: 2017-06-26 (Mon, 26 Jun 2017) Changed paths: A test-data/5_Ig-like.gff M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_attribute.xml Log Message: ----------- Merge pull request #3076 from peterjc/gff3_filter_by_attribute GFF3 support in filter by attribute Compare: https://github.com/galaxyproject/galaxy/compare/ce1316d6808e...46dbf8d10c6d

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