November 2015 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/galaxy] ad2045: Fix output to print values and not hash key
by GitHub 09 Nov '15

09 Nov '15

Branch: refs/heads/release_15.10 Home: https://github.com/galaxyproject/galaxy Commit: ad20452340d052570c1b3203259d10e1ad94a236 https://github.com/galaxyproject/galaxy/commit/ad20452340d052570c1b3203259d… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Fix output to print values and not hash key Commit: ad4458a458d7ccb5238094ab3d1967072b5a0b76 https://github.com/galaxyproject/galaxy/commit/ad4458a458d7ccb5238094ab3d19… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-09 (Fri, 09 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Revert to previous changes if using rpy2 Commit: 0ec1b17794d53ae1a535b00f13d955c62f702a94 https://github.com/galaxyproject/galaxy/commit/0ec1b17794d53ae1a535b00f13d9… Author: Eric Enns <eric.enns(a)phac-aspc.gc.ca> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Update list comprehension to go through headings instead of summary so that we output in the order we want. Commit: 50c27ace2c6eb260b88aafac72997cfa06ca6c13 https://github.com/galaxyproject/galaxy/commit/50c27ace2c6eb260b88aafac7299… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-10-14 (Wed, 14 Oct 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge pull request #885 from ericenns/fix_gsummary_in_release_15.07 [15.07] Fix gsummary in release 15.07 Commit: 57d6c9872c21f0bddfde04b170e8e8021d20ff71 https://github.com/galaxyproject/galaxy/commit/57d6c9872c21f0bddfde04b170e8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge remote-tracking branch 'jmchilton/release_15.07' into release_15.10 Commit: 7e6df4f46fe0eed8328b57543b069911e4988d02 https://github.com/galaxyproject/galaxy/commit/7e6df4f46fe0eed8328b57543b06… Author: John Chilton <jmchilton(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M tools/stats/gsummary.py Log Message: ----------- Merge pull request #1043 from jmchilton/release_15.10-forward-port [15.10] Forward port 15.07 fix to 15.10. Compare: https://github.com/galaxyproject/galaxy/compare/3b8edf6aebfb...7e6df4f46fe0

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[galaxyproject/galaxy] 76bcfa: Fix log comments
by GitHub 09 Nov '15

09 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 76bcfaa0ff85fe996ee2afccfb85e01f154e75b3 https://github.com/galaxyproject/galaxy/commit/76bcfaa0ff85fe996ee2afccfb85… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/utils/deferred.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/utils/deferred.js M static/scripts/utils/uploadbox.js Log Message: ----------- Fix log comments Use emit Fix namespace Fix namespace Remove empty line Check if logger exists Fix comment Redo More Fix yet another log Fix statements More fixes Move emitter Commit: daccea42bdbd545e6ed9d91bd4685036b95410a8 https://github.com/galaxyproject/galaxy/commit/daccea42bdbd545e6ed9d91bd468… Author: Martin Cech <cech.marten(a)gmail.com> Date: 2015-11-09 (Mon, 09 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/mvc/form/form-parameters.js M client/galaxy/scripts/mvc/form/form-repeat.js M client/galaxy/scripts/mvc/form/form-select-content.js M client/galaxy/scripts/mvc/form/form-view.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/tools/tools-form-workflow.js M client/galaxy/scripts/mvc/tools/tools-jobs.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/uploadbox.js M static/maps/galaxy-app-base.js.map M static/maps/mvc/form/form-parameters.js.map M static/maps/mvc/form/form-repeat.js.map M static/maps/mvc/form/form-select-content.js.map M static/maps/mvc/form/form-view.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/tools/tools-form-workflow.js.map M static/maps/mvc/tools/tools-jobs.js.map M static/maps/utils/deferred.js.map M static/maps/utils/uploadbox.js.map M static/scripts/galaxy-app-base.js M static/scripts/mvc/form/form-parameters.js M static/scripts/mvc/form/form-repeat.js M static/scripts/mvc/form/form-select-content.js M static/scripts/mvc/form/form-view.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/tools/tools-form-workflow.js M static/scripts/mvc/tools/tools-jobs.js M static/scripts/utils/deferred.js M static/scripts/utils/uploadbox.js Log Message: ----------- Merge pull request #1040 from guerler/revise_logging_000 Fix log statements and link to logger Compare: https://github.com/galaxyproject/galaxy/compare/c36ff5bcc7e8...daccea42bdbd

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[galaxyproject/usegalaxy-playbook] 7372b6: Dropped link to poss for GCC2016 Training Topics.
by GitHub 07 Nov '15

07 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 7372b6812790e8338eea0ea30d1a71fc623c72e4 https://github.com/galaxyproject/usegalaxy-playbook/commit/7372b6812790e833… Author: tnabtaf <clements(a)galaxyproject.org> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: M templates/galaxy/common/static/welcome.html.j2 Log Message: ----------- Dropped link to poss for GCC2016 Training Topics.

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[galaxyproject/galaxy] dc10ac: Add stub fetch_eggs.py/check_eggs.py for people wh...
by GitHub 07 Nov '15

07 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: dc10ac7e3ec3bac08eed4e786fa855c7422b8b3c https://github.com/galaxyproject/galaxy/commit/dc10ac7e3ec3bac08eed4e786fa8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: A scripts/check_eggs.py A scripts/fetch_eggs.py Log Message: ----------- Add stub fetch_eggs.py/check_eggs.py for people whose build/test/run pipelines may have been running these by hand. Print hopefully helpful information and return 1. Fixes #1030 Commit: c36ff5bcc7e840289e1d6c10610ac1dd90ddee19 https://github.com/galaxyproject/galaxy/commit/c36ff5bcc7e840289e1d6c10610a… Author: Daniel Blankenberg <dan.blankenberg(a)gmail.com> Date: 2015-11-07 (Sat, 07 Nov 2015) Changed paths: A scripts/check_eggs.py A scripts/fetch_eggs.py Log Message: ----------- Merge pull request #1037 from natefoo/smash-eggs-bugfix1 Add stub fetch_eggs.py/check_eggs.py Compare: https://github.com/galaxyproject/galaxy/compare/e2f9cf2dd6cc...c36ff5bcc7e8

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[galaxyproject/galaxy] 168d42: Keep select field open for multi select
by GitHub 06 Nov '15

06 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 168d42acf39196969c48864c9dcb43cb311eb641 https://github.com/galaxyproject/galaxy/commit/168d42acf39196969c48864c9dcb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Keep select field open for multi select Commit: f57d91794917ac7ee057585addc1891e81c40fdf https://github.com/galaxyproject/galaxy/commit/f57d91794917ac7ee057585addc1… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-03 (Tue, 03 Nov 2015) Changed paths: M client/galaxy/scripts/libs/jquery/select2.js M static/maps/libs/jquery/select2.js.map M static/scripts/libs/jquery/select2.js Log Message: ----------- Patch select2 to avoid resetting highlighted location Keep search term Commit: bbc3e943e73ebb0c8358dcf0d26ac617e68bb57c https://github.com/galaxyproject/galaxy/commit/bbc3e943e73ebb0c8358dcf0d26a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M .ci/flake8_blacklist.txt M .ci/flake8_wrapper.sh M .gitignore M client/galaxy/scripts/galaxy-app-base.js M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/mvc/app/app-analysis.js M client/galaxy/scripts/mvc/app/app-view.js M client/galaxy/scripts/mvc/base-mvc.js M client/galaxy/scripts/mvc/citation/citation-model.js M client/galaxy/scripts/mvc/collection/collection-li-edit.js M client/galaxy/scripts/mvc/collection/collection-li.js M client/galaxy/scripts/mvc/collection/collection-model.js M client/galaxy/scripts/mvc/collection/collection-panel.js M client/galaxy/scripts/mvc/collection/list-collection-creator.js M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js M client/galaxy/scripts/mvc/collection/pair-collection-creator.js M client/galaxy/scripts/mvc/dataset/dataset-choice.js M client/galaxy/scripts/mvc/dataset/dataset-li.js M client/galaxy/scripts/mvc/dataset/dataset-list.js M client/galaxy/scripts/mvc/dataset/dataset-model.js M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/history/history-content-model.js 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-panel.js M client/galaxy/scripts/mvc/history/history-structure-view.js M client/galaxy/scripts/mvc/history/multi-panel.js M client/galaxy/scripts/mvc/job/job-model.js M client/galaxy/scripts/mvc/list/list-item.js M client/galaxy/scripts/mvc/list/list-panel.js M client/galaxy/scripts/mvc/tags.js M client/galaxy/scripts/mvc/tools/tools-form-base.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/scripts/mvc/user/user-model.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/galaxy/scripts/mvc/visualization/visualization-model.js M client/galaxy/scripts/templates/compiled/tool_link.js M client/galaxy/scripts/templates/tool_link.handlebars M client/galaxy/scripts/utils/add-logging.js M client/galaxy/scripts/utils/deferred.js M client/galaxy/scripts/utils/metrics-logger.js M client/galaxy/style/less/base.less M client/galaxy/style/less/bootstrap.less M client/galaxy/style/less/ui.less M client/galaxy/style/less/upload.less M config/plugins/visualizations/charts/static/build-app.js M config/plugins/visualizations/charts/static/charts/jqplot/boxplot/wrapper.js M config/plugins/visualizations/charts/static/charts/nvd3/pie/wrapper.js M config/plugins/visualizations/charts/static/charts/tools.js M config/plugins/visualizations/charts/static/views/group.js M config/plugins/visualizations/charts/static/views/viewport.js M doc/source/lib/galaxy.auth.providers.rst M doc/source/lib/galaxy.datatypes.rst A doc/source/lib/galaxy.dependencies.rst M doc/source/lib/galaxy.eggs.rst M doc/source/lib/galaxy.jobs.runners.rst M doc/source/lib/galaxy.rst M doc/source/lib/galaxy.tools.deps.resolvers.rst M doc/source/lib/galaxy.web.framework.middleware.rst M doc/source/lib/galaxy.webapps.galaxy.controllers.rst M doc/source/lib/galaxy.webapps.reports.controllers.rst M doc/source/lib/galaxy.webapps.rst M doc/source/lib/galaxy.webapps.tool_shed.api.rst M doc/source/lib/modules.rst R doc/source/lib/pkg_resources.rst M lib/galaxy/app.py M lib/galaxy/config.py M lib/galaxy/jobs/metrics/instrumenters/collectl.py A lib/galaxy/jobs/runners/util/drmaa/__init__.py A lib/galaxy/jobs/runners/util/retry.py A lib/galaxy/jobs/runners/util/sudo.py M lib/galaxy/model/__init__.py M lib/galaxy/objectstore/__init__.py M lib/galaxy/objectstore/rods.py M lib/galaxy/objectstore/s3.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/commands.py M lib/galaxy/tools/deps/docker_util.py M lib/galaxy/tools/deps/dockerfiles.py M lib/galaxy/tools/deps/resolvers/modules.py M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py M lib/galaxy/tools/lint.py A lib/galaxy/tools/lint_util.py M lib/galaxy/tools/linters/command.py M lib/galaxy/tools/linters/help.py M lib/galaxy/tools/linters/inputs.py M lib/galaxy/tools/linters/outputs.py A lib/galaxy/tools/linters/stdio.py M lib/galaxy/tools/linters/tests.py M lib/galaxy/tools/linters/top_level.py A lib/galaxy/tools/linters/xml_order.py M lib/galaxy/tools/loader_directory.py M lib/galaxy/tools/search/__init__.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/util/__init__.py M lib/galaxy/util/xml_macros.py M lib/galaxy/webapps/galaxy/api/library_contents.py M lib/galaxy/webapps/galaxy/controllers/requests_common.py M lib/galaxy/webapps/reports/app.py M lib/galaxy/webapps/tool_shed/app.py M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py M lib/pulsar/client/transport/curl.py M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py M lib/tool_shed/galaxy_install/tool_migration_manager.py M lib/tool_shed/util/common_util.py M lib/tool_shed/util/hg_util.py M run.sh M scripts/tools/maf/check_loc_file.py M static/maps/galaxy-app-base.js.map M static/maps/mvc/app/app-analysis.js.map M static/maps/mvc/app/app-view.js.map M static/maps/mvc/base-mvc.js.map M static/maps/mvc/citation/citation-model.js.map M static/maps/mvc/collection/collection-model.js.map M static/maps/mvc/collection/collection-panel.js.map M static/maps/mvc/collection/list-collection-creator.js.map M static/maps/mvc/collection/list-of-pairs-collection-creator.js.map M static/maps/mvc/collection/pair-collection-creator.js.map M static/maps/mvc/dataset/dataset-choice.js.map M static/maps/mvc/dataset/dataset-li.js.map M static/maps/mvc/dataset/dataset-list.js.map M static/maps/mvc/dataset/dataset-model.js.map M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/history/history-content-model.js.map M static/maps/mvc/history/history-contents.js.map M static/maps/mvc/history/history-model.js.map M static/maps/mvc/history/history-panel.js.map M static/maps/mvc/history/history-structure-view.js.map M static/maps/mvc/history/multi-panel.js.map M static/maps/mvc/job/job-model.js.map M static/maps/mvc/list/list-item.js.map M static/maps/mvc/list/list-panel.js.map M static/maps/mvc/tags.js.map M static/maps/mvc/tools/tools-form-base.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/maps/mvc/upload/upload-button.js.map M static/maps/mvc/user/user-model.js.map M static/maps/mvc/user/user-quotameter.js.map M static/maps/mvc/visualization/visualization-model.js.map M static/maps/templates/compiled/tool_link.js.map M static/maps/utils/add-logging.js.map M static/maps/utils/deferred.js.map M static/maps/utils/metrics-logger.js.map M static/scripts/galaxy-app-base.js M static/scripts/galaxy.panels.js M static/scripts/mvc/app/app-analysis.js M static/scripts/mvc/base-mvc.js M static/scripts/mvc/citation/citation-model.js M static/scripts/mvc/collection/collection-model.js M static/scripts/mvc/collection/collection-panel.js M static/scripts/mvc/collection/list-collection-creator.js M static/scripts/mvc/collection/list-of-pairs-collection-creator.js M static/scripts/mvc/collection/pair-collection-creator.js M static/scripts/mvc/dataset/dataset-choice.js M static/scripts/mvc/dataset/dataset-li.js M static/scripts/mvc/dataset/dataset-list.js M static/scripts/mvc/dataset/dataset-model.js M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/history/history-content-model.js M static/scripts/mvc/history/history-contents.js M static/scripts/mvc/history/history-model.js M static/scripts/mvc/history/history-panel.js M static/scripts/mvc/history/history-structure-view.js M static/scripts/mvc/history/multi-panel.js M static/scripts/mvc/job/job-model.js M static/scripts/mvc/list/list-item.js M static/scripts/mvc/list/list-panel.js M static/scripts/mvc/tools/tools-form-base.js M static/scripts/mvc/ui/ui-select-default.js M static/scripts/mvc/upload/upload-button.js M static/scripts/mvc/user/user-model.js M static/scripts/mvc/user/user-quotameter.js M static/scripts/templates/compiled/tool_link.js M static/scripts/utils/add-logging.js M static/scripts/utils/deferred.js M static/scripts/utils/metrics-logger.js M static/style/blue/base.css M templates/galaxy_client_app.mako M test/api/helpers.py M test/qunit/tests/galaxy-app-base.js M tools/data_source/data_source.py M tools/evolution/add_scores.py M tools/extract/extract_genomic_dna.py M tools/extract/liftOver_wrapper.py M tools/filters/axt_to_concat_fasta.py M tools/filters/axt_to_fasta.py M tools/filters/axt_to_lav.py M tools/filters/catWrapper.py M tools/filters/gff/extract_GFF_Features.py M tools/filters/gff/gff_filter_by_attribute.py M tools/filters/gff/gff_filter_by_feature_count.py M tools/filters/gff/sort_gtf.py M tools/filters/gff_to_bed_converter.py M tools/filters/lav_to_bed.py M tools/filters/secure_hash_message_digest.py M tools/filters/wiggle_to_simple.py M tools/genomespace/genomespace_exporter.py M tools/maf/interval2maf.py M tools/maf/interval2maf.xml M tools/maf/interval_maf_to_merged_fasta.py M tools/maf/maf_by_block_number.py M tools/maf/maf_filter.py M tools/maf/maf_limit_size.py M tools/maf/maf_limit_to_species.py M tools/maf/maf_reverse_complement.py M tools/maf/maf_split_by_species.py M tools/maf/maf_stats.py M tools/maf/maf_thread_for_species.py M tools/maf/maf_to_bed.py M tools/maf/maf_to_bed_code.py M tools/maf/maf_to_fasta_concat.py M tools/maf/maf_to_fasta_multiple_sets.py M tools/maf/maf_to_interval.py M tools/maf/vcf_to_maf_customtrack.py M tools/next_gen_conversion/fastq_conversions.py M tools/next_gen_conversion/fastq_gen_conv.py M tools/next_gen_conversion/solid2fastq.py M tools/next_gen_conversion/solid_to_fastq.py M tools/ngs_simulation/ngs_simulation.py M tools/stats/aggregate_scores_in_intervals.py M tools/stats/filtering.py M tools/stats/grouping.py M tools/stats/gsummary.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into revise_multiselect_000 Commit: 975a94ce016811ff08eb1e9ac75b4463277e6199 https://github.com/galaxyproject/galaxy/commit/975a94ce016811ff08eb1e9ac75b… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Pack scripts Commit: e2f9cf2dd6cca01a4fccc92ff746ea00fa1e3dd0 https://github.com/galaxyproject/galaxy/commit/e2f9cf2dd6cca01a4fccc92ff746… Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: M client/galaxy/scripts/libs/jquery/select2.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M static/maps/libs/jquery/select2.js.map M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/libs/jquery/select2.js M static/scripts/mvc/ui/ui-select-default.js Log Message: ----------- Merge pull request #1019 from guerler/revise_multiselect_000 Keep select field open for multi select Compare: https://github.com/galaxyproject/galaxy/compare/1498ca2364ff...e2f9cf2dd6cc

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[galaxyproject/galaxy] 8231df: Add 2 missing dependencies of dependencies
by GitHub 06 Nov '15

06 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 8231df01fac0bf9596cfb6bc3c3586c0baffbe6f https://github.com/galaxyproject/galaxy/commit/8231df01fac0bf9596cfb6bc3c35… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-10-29 (Thu, 29 Oct 2015) Changed paths: M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Add 2 missing dependencies of dependencies Commit: a2d30648c9a83c776937cd78d9ae470d6a155094 https://github.com/galaxyproject/galaxy/commit/a2d30648c9a83c776937cd78d9ae… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt Log Message: ----------- Add importlib and ordereddict for Python 2.6. They won't be installed by conditional since they will always be installed as dependencies of kombu in requirements.txt. This should be fixed at some point. Commit: ff3501243978a9c949eb7f0bd9b1443aad17163e https://github.com/galaxyproject/galaxy/commit/ff3501243978a9c949eb7f0bd9b1… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-02 (Mon, 02 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py Log Message: ----------- XPath support is not the same on all Python 2.6es Commit: 1498ca2364ff7f64841fea44aa53758dcb880d45 https://github.com/galaxyproject/galaxy/commit/1498ca2364ff7f64841fea44aa53… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-06 (Fri, 06 Nov 2015) Changed paths: M lib/galaxy/dependencies/__init__.py M lib/galaxy/dependencies/conditional-requirements.txt M lib/galaxy/dependencies/requirements.txt Log Message: ----------- Merge pull request #1006 from natefoo/smash_eggs Add 2 missing dependencies of dependencies Compare: https://github.com/galaxyproject/galaxy/compare/f69c06b6cf6d...1498ca2364ff

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[galaxyproject/galaxy] 4908a5: wig_to_bigwig: Add error message for wrongly forma...
by GitHub 05 Nov '15

05 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 4908a5bab6578137521c13932c799719648f2351 https://github.com/galaxyproject/galaxy/commit/4908a5bab6578137521c13932c79… Author: Jelle Scholtalbers <j.scholtalbers(a)gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M tools/filters/wig_to_bigwig.xml Log Message: ----------- wig_to_bigwig: Add error message for wrongly formatted data Commit: f69c06b6cf6dfa1635743c35901bd1f57b3b4f21 https://github.com/galaxyproject/galaxy/commit/f69c06b6cf6dfa1635743c35901b… Author: Nicola Soranzo <nsoranzo(a)tiscali.it> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M tools/filters/wig_to_bigwig.xml Log Message: ----------- Merge pull request #1033 from scholtalbers/wig_to_bigwig_error_msg wig_to_bigwig: Add error message for wrongly formatted data Compare: https://github.com/galaxyproject/galaxy/compare/596247627516...f69c06b6cf6d

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[galaxyproject/usegalaxy-playbook] 9f9961: Test mutable configs
by GitHub 05 Nov '15

05 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 9f99615b50b892da2d96fb62bf684dbc569ef010 https://github.com/galaxyproject/usegalaxy-playbook/commit/9f99615b50b892da… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml M files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml Log Message: ----------- Test mutable configs Commit: e8809829b129803cbbfdf1979dbb6c5219110a87 https://github.com/galaxyproject/usegalaxy-playbook/commit/e8809829b129803c… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M files/galaxy/common/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/common/dynamic_rules/reserved.py M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Add Anton to reserved users, increased reserved job limits on Test Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/5e9e49fcd98c...…

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[galaxyproject/galaxy] 771765: Allow resizing of regular multi-select boxes
by GitHub 05 Nov '15

05 Nov '15

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 7717659c784085a772565d028c77c73b48a54630 https://github.com/galaxyproject/galaxy/commit/7717659c784085a772565d028c77… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/build-app.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/galaxy.panels.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Allow resizing of regular multi-select boxes Remove event handler Add mouse leave event handler Improve visibility and accessibility Fix tag name Style compromise Repack charts Commit: 8a9372b989b35a049ceec721846ae0811a8f8cfe https://github.com/galaxyproject/galaxy/commit/8a9372b989b35a049ceec721846a… Author: guerler <aysam.guerler(a)gmail.com> Date: 2015-11-04 (Wed, 04 Nov 2015) Changed paths: M client/galaxy/scripts/mvc/grid/grid-template.js M client/galaxy/scripts/mvc/upload/upload-button.js M client/galaxy/style/less/base.less M client/galaxy/style/less/upload.less M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py M run.sh M static/maps/mvc/grid/grid-template.js.map M static/maps/mvc/upload/upload-button.js.map M static/scripts/mvc/grid/grid-template.js M static/scripts/mvc/upload/upload-button.js M static/style/blue/base.css M test/api/helpers.py Log Message: ----------- Merge branch 'dev' of https://github.com/galaxyproject/galaxy into revise_multiselect_001 Commit: 59624762751624c831e0b60a3fde1fdf9d4a78f9 https://github.com/galaxyproject/galaxy/commit/59624762751624c831e0b60a3fde… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M client/galaxy/scripts/galaxy.panels.js M client/galaxy/scripts/mvc/ui/ui-select-default.js M client/galaxy/style/less/base.less M client/galaxy/style/less/ui.less M config/plugins/visualizations/charts/static/build-app.js M static/maps/mvc/ui/ui-select-default.js.map M static/scripts/galaxy.panels.js M static/scripts/mvc/ui/ui-select-default.js M static/style/blue/base.css Log Message: ----------- Merge pull request #1025 from guerler/revise_multiselect_001 Allow resizing of regular multi-select boxes Compare: https://github.com/galaxyproject/galaxy/compare/afa65f4d9a36...596247627516

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[galaxyproject/infrastructure-playbook] 6d10ce: Whoops, there is no `group_users`.
by GitHub 04 Nov '15

04 Nov '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/infrastructure-playbook Commit: 6d10ce184dc53a0d427e6a51c0af75613be61a0a https://github.com/galaxyproject/infrastructure-playbook/commit/6d10ce184dc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-11-05 (Thu, 05 Nov 2015) Changed paths: M galaxyenv/group_vars/starforgebuilders.yml Log Message: ----------- Whoops, there is no `group_users`.

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