Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 77c34446728f414491dd7a14fc5992800d9ae32a
https://github.com/galaxyproject/galaxy/commit/77c34446728f414491dd7a14fc59…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Add webapp mapper for cloud upload API.
Commit: 92830a1c155450a68bdd5d214d3f432f00056a1c
https://github.com/galaxyproject/galaxy/commit/92830a1c155450a68bdd5d214d3f…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/cloud.py
Log Message:
-----------
Implement cloud upload API.
Commit: 4e23c5e67dbc57ff03512f65549d6ea097a70deb
https://github.com/galaxyproject/galaxy/commit/4e23c5e67dbc57ff03512f65549d…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/managers/cloud.py
Log Message:
-----------
Implement logic of uploading dataset(s) to cloud in the cloud manager.
Commit: 62d67c9c401c2c5c1547457fe82229cf97e7e0ff
https://github.com/galaxyproject/galaxy/commit/62d67c9c401c2c5c1547457fe822…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/cloud.py
Log Message:
-----------
Check for missing arguments from payload in cloud upload api.
Commit: 63be2dba410c1d1cc17e6e4a1030d100bf5eaf6b
https://github.com/galaxyproject/galaxy/commit/63be2dba410c1d1cc17e6e4a1030…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/cloud.py
Log Message:
-----------
Assert the validity of provided history ID in cloud upload API.
Commit: 6a9ce39a2147b0b2449e4eaf73fb6e54399b5976
https://github.com/galaxyproject/galaxy/commit/6a9ce39a2147b0b2449e4eaf73fb…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/cloud.py
Log Message:
-----------
Assert the validity of provided dataset ID(s).
Commit: ff42cc7b0684c47191a94e4d1a016dcbc7ef21b1
https://github.com/galaxyproject/galaxy/commit/ff42cc7b0684c47191a94e4d1a01…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/managers/cloud.py
M lib/galaxy/webapps/galaxy/api/cloud.py
Log Message:
-----------
In cloud upload API, handle overwriting an existing object.
Commit: f1b9a23c939f20718b430916e5e5fdd4d9b2a330
https://github.com/galaxyproject/galaxy/commit/f1b9a23c939f20718b430916e5e5…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/cloud.py
Log Message:
-----------
Use named arguments in cloud upload API when calling its manager.
Commit: 35a30219f652741e20f6810b42c21dbf3e74e0c0
https://github.com/galaxyproject/galaxy/commit/35a30219f652741e20f6810b42c2…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/managers/cloud.py
Log Message:
-----------
Fix a bug in cloud upload API.
Commit: 17ab3e8d2dff82996264a3404fda800a707b8487
https://github.com/galaxyproject/galaxy/commit/17ab3e8d2dff82996264a3404fda…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/cloud.py
Log Message:
-----------
Update cloud upload API description.
Commit: 0ed19ad7b0402c7be544a358386b80377d63d85c
https://github.com/galaxyproject/galaxy/commit/0ed19ad7b0402c7be544a358386b…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/managers/cloud.py
M lib/galaxy/webapps/galaxy/api/cloud.py
Log Message:
-----------
Update cloud upload API description.
Commit: 3b74bd899c323f99135362a23f64726cd09ee331
https://github.com/galaxyproject/galaxy/commit/3b74bd899c323f99135362a23f64…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-05-07 (Mon, 07 May 2018)
Changed paths:
M lib/galaxy/managers/cloud.py
Log Message:
-----------
Fix bugs related to import order and boolean assert in cloud upload API.
Commit: c7c7691c98b2ef2cdeee5bf7661b9415e6eebf86
https://github.com/galaxyproject/galaxy/commit/c7c7691c98b2ef2cdeee5bf7661b…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M .ci/flake8_blacklist.txt
M .ci/jenkins/selenium/run_tests.sh
M .gitignore
M .travis.yml
M Makefile
M client/GruntFile.js
M client/bower.json
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A client/galaxy/docs/galaxy-buttons.md
A client/galaxy/docs/galaxy-forms.md
A client/galaxy/docs/galaxy-masthead.md
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A client/galaxy/docs/galaxy-messages.md
A client/galaxy/docs/galaxy-panels.md
A client/galaxy/docs/galaxy-tables.md
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M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
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M client/galaxy/scripts/apps/panels/tool-panel.js
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M client/galaxy/scripts/components/HistoryImport.vue
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M client/galaxy/scripts/components/RuleCollectionBuilder.vue
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M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/legacy/grid/grid-view.js
R client/galaxy/scripts/libs/bootstrap-tour.js
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M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
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M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/job-dag.js
M client/galaxy/scripts/mvc/history/job-states-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
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M client/galaxy/scripts/mvc/library/library-librarylist-view.js
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M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/list/list-view.js
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M client/galaxy/scripts/mvc/tag.js
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M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
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M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/ui/ui-select.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/scripts/mvc/upload/collection/collection-row.js
M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/visualization/chart/components/model.js
M client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js
M client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
M client/galaxy/scripts/mvc/visualization/chart/utilities/series.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-connector.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/qunit/test-app.js
M client/galaxy/scripts/qunit/tests/form_tests.js
M client/galaxy/scripts/qunit/tests/masthead_tests.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/reports/run_stats.js
M client/galaxy/scripts/toolshed/groups/group-detail-view.js
M client/galaxy/scripts/toolshed/groups/group-list-view.js
M client/galaxy/scripts/ui/filter-control.js
M client/galaxy/scripts/utils/async-save-text.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/visualization.js
R client/galaxy/style/less/autocomplete_tagging.less
R client/galaxy/style/less/base.less
R client/galaxy/style/less/bootstrap.less
R client/galaxy/style/less/bootstrap/alerts.less
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R client/galaxy/style/less/bootstrap/button-groups.less
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R client/galaxy/style/less/galaxy_variables.less
R client/galaxy/style/less/history.less
R client/galaxy/style/less/iconic_stroke.less
R client/galaxy/style/less/job.less
R client/galaxy/style/less/jstree.less
R client/galaxy/style/less/library.less
R client/galaxy/style/less/list-item.less
R client/galaxy/style/less/reports.less
R client/galaxy/style/less/select2.less
R client/galaxy/style/less/theme/blue.less
R client/galaxy/style/less/theme/plain.less
R client/galaxy/style/less/toastr.less
R client/galaxy/style/less/tour.less
R client/galaxy/style/less/trackster.less
R client/galaxy/style/less/ui.less
R client/galaxy/style/less/ui/dataset-choice.less
R client/galaxy/style/less/ui/error-modal.less
R client/galaxy/style/less/ui/icon-btn.less
R client/galaxy/style/less/ui/pagination.less
R client/galaxy/style/less/ui/paired-collection-creator.less
R client/galaxy/style/less/ui/peek-column-selector.less
R client/galaxy/style/less/ui/search-input.less
R client/galaxy/style/less/upload.less
A client/galaxy/style/scss/autocomplete_tagging.scss
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A client/galaxy/style/scss/galaxy_bootstrap/overrides.scss
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M client/package.json
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M config/containers_conf.yml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
M config/job_conf.xml.sample_basic
M config/job_metrics_conf.xml.sample
M config/local_conda_mapping.yml.sample
A config/oidc_backends_config.xml.sample
A config/oidc_config.xml.sample
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M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/tours/core.scratchbook.yaml
M config/plugins/visualizations/common/templates/chart_entry_point.mako
M config/plugins/visualizations/csg/templates/csg.mako
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M config/plugins/visualizations/drawrna/config/drawrna.xml
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M config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml
M config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml
M config/plugins/visualizations/heatmap/heatmap_default/src/script.js
M config/plugins/visualizations/heatmap/heatmap_default/static/script.js
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A config/plugins/visualizations/hivtrace/static/448c34a56d699c29117adc64c43affeb.woff2
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M config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml
M config/plugins/visualizations/jqplot/jqplot_bar/src/script.js
M config/plugins/visualizations/jqplot/jqplot_bar/static/script.css
M config/plugins/visualizations/jqplot/jqplot_bar/static/script.js
M config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
M config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
M config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml
M config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml
M config/plugins/visualizations/msa/config/msa.xml
M config/plugins/visualizations/ngl/config/ngl.xml
M config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml
M config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml
M config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
M config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
M config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml
M config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml
M config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml
M config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml
M config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml
M config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml
M config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml
M config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml
M config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml
M config/plugins/visualizations/phylocanvas/config/phylocanvas.xml
M config/plugins/visualizations/pv/config/pv.xml
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
M config/plugins/visualizations/unipept/templates/unipept.mako
M config/plugins/visualizations/venn/config/venn.xml
M config/plugins/webhooks/demo/search/script.js
M config/reports.yml.sample
M config/tool_conf.xml.main
M config/tool_conf.xml.sample
M config/tool_data_table_conf.xml.sample
M config/tool_destinations.yml.sample
M config/tool_shed.yml.sample
M create_db.sh
M display_applications/igb/bam.xml
M display_applications/igb/bb.xml
M display_applications/igb/bed.xml
M display_applications/igb/bedgraph.xml
M display_applications/igb/bigwig.xml
M display_applications/igb/gtf.xml
M display_applications/igb/wig.xml
A display_applications/intermine/intermine_simple.xml
M doc/parse_gx_xsd.py
M doc/source/admin/authentication.md
M doc/source/admin/cluster.md
M doc/source/admin/framework_dependencies.rst
M doc/source/admin/galaxy_options.rst
M doc/source/admin/jobs.md
M doc/source/admin/reports_options.rst
M doc/source/admin/scaling.md
M doc/source/admin/special_topics/bug_reports.rst
A doc/source/admin/special_topics/gdpr_compliance.rst
M doc/source/admin/special_topics/index.rst
M doc/source/admin/special_topics/performance_tracking.rst
M doc/source/conf.versioning.py
M doc/source/lib/galaxy.web.framework.middleware.rst
M doc/source/project/organization.rst
A doc/source/releases/18.05.rst
M doc/source/releases/18.05_announce.rst
M doc/source/releases/index.rst
M extract_dataset_parts.sh
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/alwaysreject.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/localdb.py
M lib/galaxy/auth/providers/pam_auth.py
A lib/galaxy/authnz/__init__.py
A lib/galaxy/authnz/managers.py
A lib/galaxy/authnz/psa_authnz.py
M lib/galaxy/config.py
M lib/galaxy/containers/__init__.py
M lib/galaxy/containers/docker.py
M lib/galaxy/containers/docker_model.py
M lib/galaxy/containers/docker_swarm.py
R lib/galaxy/containers/docker_swarm_manager.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/dataset_collections/subcollections.py
M lib/galaxy/dataset_collections/type_description.py
M lib/galaxy/datatypes/annotation.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/blast.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
A lib/galaxy/datatypes/converters/bam_to_bai.xml
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bed_gff_or_vcf_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/bedgraph_to_bigwig_converter.xml
A lib/galaxy/datatypes/converters/bz2_to_uncompressed.xml
M lib/galaxy/datatypes/converters/fasta_to_2bit.xml
M lib/galaxy/datatypes/converters/fasta_to_fai.xml
R lib/galaxy/datatypes/converters/fastagz_to_fasta.xml
R lib/galaxy/datatypes/converters/fastqbz2_to_fastq.xml
R lib/galaxy/datatypes/converters/fastqcssangerbz2_to_fastqcssanger.xml
R lib/galaxy/datatypes/converters/fastqcssangergz_to_fastqcssanger.xml
R lib/galaxy/datatypes/converters/fastqgz_to_fastq.xml
R lib/galaxy/datatypes/converters/fastqilluminabz2_to_fastqillumina.xml
R lib/galaxy/datatypes/converters/fastqilluminagz_to_fastqillumina.xml
R lib/galaxy/datatypes/converters/fastqsangerbz2_to_fastqsanger.xml
R lib/galaxy/datatypes/converters/fastqsangergz_to_fastqsanger.xml
R lib/galaxy/datatypes/converters/fastqsolexabz2_to_fastqsolexa.xml
R lib/galaxy/datatypes/converters/fastqsolexagz_to_fastqsolexa.xml
R lib/galaxy/datatypes/converters/genbankgz_to_genbank.xml
A lib/galaxy/datatypes/converters/gz_to_uncompressed.xml
M lib/galaxy/datatypes/converters/interval_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/wig_to_bigwig_converter.xml
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/display_applications/util.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/phylip.py
M lib/galaxy/datatypes/plant_tribes.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/1.afg
A lib/galaxy/datatypes/test/1.arff
A lib/galaxy/datatypes/test/1.fastqsanger.bz2
A lib/galaxy/datatypes/test/1.fastqsanger.gz
A lib/galaxy/datatypes/test/1.hdt
A lib/galaxy/datatypes/test/1.obo
A lib/galaxy/datatypes/test/1.owl
A lib/galaxy/datatypes/test/1.phyloxml
A lib/galaxy/datatypes/test/1.stockholm
A lib/galaxy/datatypes/test/1.tiff
A lib/galaxy/datatypes/test/1.ttl
A lib/galaxy/datatypes/test/1.xmfa
A lib/galaxy/datatypes/test/2.tabular
A lib/galaxy/datatypes/test/2.txt
A lib/galaxy/datatypes/test/3.txt
A lib/galaxy/datatypes/test/Acanium.hmm
A lib/galaxy/datatypes/test/diamond.daa
A lib/galaxy/datatypes/test/empty.txt
M lib/galaxy/datatypes/test/example.iqtree
A lib/galaxy/datatypes/test/test.blib
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/triples.py
M lib/galaxy/datatypes/upload_util.py
M lib/galaxy/datatypes/xml.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conda-file.sh
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pipfiles/default/Pipfile
M lib/galaxy/dependencies/pipfiles/default/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/develop/Pipfile
R lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
R lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
A lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/dynamic_tool_destination.py
R lib/galaxy/jobs/error_level.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/instrumenters/cgroup.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/core.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/env.py
A lib/galaxy/jobs/metrics/instrumenters/hostname.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/metrics/instrumenters/uname.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/util/cli/job/slurm.py
M lib/galaxy/jobs/runners/util/cli/job/torque.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
R lib/galaxy/jobs/runners/util/drmaa/__init__.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
R lib/galaxy/jobs/runners/util/retry.py
M lib/galaxy/managers/base.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/cloud.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/versions/0136_collection_and_workflow_state.py
A lib/galaxy/model/migrate/versions/0141_add_oidc_tables.py
A lib/galaxy/model/migrate/versions/0142_change_numeric_metric_precision.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/queue_worker.py
M lib/galaxy/security/__init__.py
M lib/galaxy/security/passwords.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/upload.py
A lib/galaxy/tools/apply_rules.xml
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_fetch.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml
M lib/galaxy/tools/error_reports/plugins/biostars.py
M lib/galaxy/tools/error_reports/plugins/email.py
M lib/galaxy/tools/error_reports/plugins/github.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/errors.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
A lib/galaxy/tools/filter_empty_collection.xml
M lib/galaxy/tools/filter_failed_collection.xml
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dataset_matcher.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/history_query.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/wrapped_json.py
M lib/galaxy/tools/parser/cwl.py
A lib/galaxy/tools/parser/error_level.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/util.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/relabel_from_file.xml
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/interactor.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/__init__.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/compression_utils.py
M lib/galaxy/util/create_history_template.py
M lib/galaxy/util/json.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/util/permutations.py
A lib/galaxy/util/rules_dsl.py
A lib/galaxy/util/watcher.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
M lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
R lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/cloud.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/config_watchers.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
A lib/galaxy/webapps/galaxy/controllers/authnz.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/interactive_environments.py
M lib/galaxy/webapps/galaxy/controllers/page.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/reports/config_schema.yml
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/repository_revisions.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/config_schema.yml
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/modules.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/dependencies/repository/relation_builder.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/repository_review_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/repository_registry.py
M lib/tool_shed/repository_types/metadata.py
M lib/tool_shed/repository_types/repository_suite_definition.py
M lib/tool_shed/repository_types/tool_dependency_definition.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/admin_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/common_util.py
M lib/tool_shed/util/encoding_util.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/metadata_util.py
M lib/tool_shed/util/readme_util.py
M lib/tool_shed/util/repository_content_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/review_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/web_util.py
M manage_db.sh
M run.sh
M run_reports.sh
M run_tests.sh
M run_tool_shed.sh
M scripts/api/common.py
M scripts/bootstrap_history.py
M scripts/check_python.py
M scripts/cleanup_datasets/delete_datasets.sh
M scripts/cleanup_datasets/delete_userless_histories.sh
M scripts/cleanup_datasets/purge_datasets.sh
M scripts/cleanup_datasets/purge_folders.sh
M scripts/cleanup_datasets/purge_histories.sh
M scripts/cleanup_datasets/purge_libraries.sh
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
R scripts/common_startup_variables.sh
A scripts/docker_swarm_manager.py
M scripts/get_uwsgi_args.py
M scripts/grt/export.py
M scripts/grt/grt.yml.sample
M scripts/grt/upload.py
M scripts/maintenance.sh
A scripts/plugin_staging.py
A static/images/fonts/FontAwesome.otf
M static/images/fonts/fontawesome-webfont.eot
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M static/style/blue/autocomplete_tagging.css
M static/style/blue/base.css
M static/style/blue/circster.css
M static/style/blue/embed_item.css
M static/style/blue/library.css
M static/style/blue/reports.css
M static/style/blue/trackster.css
M static/welcome.html.sample
R templates/admin/impersonate.mako
R templates/admin/view_data_tables_registry.mako
R templates/admin/view_datatypes_registry.mako
M templates/base/base_panels.mako
M templates/display_common.mako
M templates/ind_share_base.mako
R templates/sharing_base.mako
M templates/show_params.mako
M templates/tagging_common.mako
M templates/user/login.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/admin/view_display_applications.mako
M templates/webapps/galaxy/data_manager/index.mako
M templates/webapps/galaxy/dataset/copy_view.mako
M templates/webapps/galaxy/galaxy.panels.mako
R templates/webapps/galaxy/history/structure.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/reports/index.mako
M templates/webapps/tool_shed/base_panels.mako
M templates/webapps/tool_shed/common/grid_common.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/view_repository.mako
M templates/webapps/tool_shed/user/manage_email_alerts.mako
A test-data/1.tiff
A test-data/filter1_in6.bed
A test-data/filter1_test6.bed
A test-data/rules/treated1fb.txt
A test-data/rules/treated2fb.txt
A test-data/rules/treated3fb.txt
M test-data/rules/uniprot.json
A test-data/rules/untreated1fb.txt
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A test-data/sort_out1.bed
A test-data/sort_out2.bed
A test-data/sort_out3.tab
A test-data/sort_out4.sam
M test/api/test_jobs.py
M test/api/test_libraries.py
M test/api/test_tools.py
M test/api/test_tools_upload.py
M test/api/test_workflows.py
A test/base/data/rules_dsl_spec.yml
M test/base/populators.py
A test/base/rules_test_data.py
A test/base/workflow_fixtures.py
M test/base/workflows_format_2/main.py
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
M test/functional/test_data_managers.py
M test/functional/test_toolbox.py
A test/functional/tools/collection_paired_conditional_structured_like.xml
A test/functional/tools/collection_paired_structured_like.xml
A test/functional/tools/collection_type_source_map_over.xml
A test/functional/tools/empty_select.xml
M test/functional/tools/for_workflows/cat_collection.xml
A test/functional/tools/identifier_single_in_repeat.xml
A test/functional/tools/inputs_as_json_with_paths.xml
M test/functional/tools/job_properties.xml
M test/functional/tools/multi_data_optional.xml
A test/functional/tools/output_action_change_format_paired.xml
R test/functional/tools/paired_collection_map_over_structured_like.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/galaxy_selenium/components.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
M test/galaxy_selenium/smart_components.py
M test/integration/test_scripts.py
M test/integration/test_upload_configuration_options.py
R test/selenium_tests/_workflow_fixtures.py
M test/selenium_tests/framework.py
A test/selenium_tests/test_admin_app.py
M test/selenium_tests/test_library_landing.py
M test/selenium_tests/test_registration.py
M test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.py
M test/unit/config/1607_root_filters/config/galaxy.ini
M test/unit/config/1607_root_samples/config/galaxy.ini
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/test_bam.py
A test/unit/datatypes/test_datatypes_registry.py
M test/unit/jobs/test_job_output_checker.py
M test/unit/jobs/test_runner_params.py
M test/unit/test_galaxy_mapping.py
M test/unit/test_remote_shell.py
A test/unit/test_rule_utils.py
M test/unit/test_security_helper.py
A test/unit/test_security_passwords.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parsing.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_deps.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/unittest_utils/tempfilecache.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_extract_summary.py
M test/unit/workflows/test_modules.py
A tool-data/intermine_simple_display.loc.sample
A tools/data_source/intermine.xml
M tools/data_source/upload.py
M tools/evolution/codingSnps.xml
M tools/extract/extract_genomic_dna.xml
M tools/extract/liftOver_wrapper.xml
M tools/filters/bed_to_bigbed.xml
M tools/filters/cutWrapper.pl
M tools/filters/sorter.py
M tools/filters/sorter.xml
M tools/filters/wig_to_bigwig.xml
M tools/phenotype_association/gpass.xml
M tools/phenotype_association/lps.xml
M tools/phenotype_association/master2gd_snp.xml
M tools/phenotype_association/master2pg.xml
M tools/sr_mapping/bfast_wrapper.xml
M tools/stats/filtering.py
M tools/stats/filtering.xml
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into upload_to_cloud
Commit: 5b1b4314a3ac140779146286f4dc2cfd5fad6807
https://github.com/galaxyproject/galaxy/commit/5b1b4314a3ac140779146286f4dc…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Refactor the API end point from `upload` to `copy_to`.
Commit: 97fd2088faa0eda1275448d7552a47c801ab9a4b
https://github.com/galaxyproject/galaxy/commit/97fd2088faa0eda1275448d7552a…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M lib/galaxy/webapps/galaxy/api/cloud.py
Log Message:
-----------
Add cloud storage `copy_to` API.
Commit: 7e8be2ff53e9f6f781618c2182d9b3d58675c47e
https://github.com/galaxyproject/galaxy/commit/7e8be2ff53e9f6f781618c2182d9…
Author: vjalili <jalili.vahid(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M lib/galaxy/managers/cloud.py
Log Message:
-----------
Add cloud-based storage `copy-to` manager.
Commit: b3f1a7cf9cdc29bcc52a6d7f5c35fc6ecfa02878
https://github.com/galaxyproject/galaxy/commit/b3f1a7cf9cdc29bcc52a6d7f5c35…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M lib/galaxy/managers/cloud.py
M lib/galaxy/webapps/galaxy/api/cloud.py
Log Message:
-----------
Doc style updates; copy-to return dict with copied datasets
Commit: 4a8857e4f9daf15101270724375dad14c4897e6c
https://github.com/galaxyproject/galaxy/commit/4a8857e4f9daf15101270724375d…
Author: Enis Afgan <afgane(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M lib/galaxy/managers/cloud.py
M lib/galaxy/webapps/galaxy/api/cloud.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
Merge pull request #6078 from VJalili/upload_to_cloud
Upload data to a cloud-based storage
Compare: https://github.com/galaxyproject/galaxy/compare/2abb01b6cbb1...4a8857e4f9da
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 603b2365b6a261e5603c618c637cf8458e667007
https://github.com/galaxyproject/galaxy/commit/603b2365b6a261e5603c618c637c…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-06-21 (Thu, 21 Jun 2018)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
Force standard HTTPTransport for sentry -- this plays nicer with a wider array of uwsgi configurations
Commit: f94a073e86be608916ec7ae79285da06ee82483b
https://github.com/galaxyproject/galaxy/commit/f94a073e86be608916ec7ae79285…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-06-21 (Thu, 21 Jun 2018)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Make sure that the workflow step has a proper state available
Commit: 3fe88a9bfe1b010ca30ffac32e5c4e200398c48e
https://github.com/galaxyproject/galaxy/commit/3fe88a9bfe1b010ca30ffac32e5c…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-07-05 (Thu, 05 Jul 2018)
Changed paths:
M lib/galaxy/visualization/plugins/interactive_environments.py
Log Message:
-----------
Merge pull request #6465 from dannon/backport-gie-static-again
[18.05] Backport of IE static url fix (to actual 18.05)
Commit: bc95f2563601635cfa1daa686b3d5c4e3ebb51ea
https://github.com/galaxyproject/galaxy/commit/bc95f2563601635cfa1daa686b3d…
Author: Devon Ryan <dpryan79(a)gmail.com>
Date: 2018-07-09 (Mon, 09 Jul 2018)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Fix the --log-file option in the job handlers
(cherry picked from commit 97c344a17a0188a687629103feefcdf03af8e768)
Commit: 23666c94a22b816bc5238e4a22c759a11265f7aa
https://github.com/galaxyproject/galaxy/commit/23666c94a22b816bc5238e4a22c7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-11 (Wed, 11 Jul 2018)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Merge pull request #6477 from natefoo/backport-pr-6351
[18.01] Fix the --log-file option in the job handlers
Commit: 93fc3a63507d6cd7c85a99ad62e71b14d4d6265e
https://github.com/galaxyproject/galaxy/commit/93fc3a63507d6cd7c85a99ad62e7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-11 (Wed, 11 Jul 2018)
Changed paths:
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Merge pull request #6369 from guerler/pages
[18.05] Make sure that the workflow step has a proper state available
Commit: 20565a2b8517fbc4c54524fa0ae127c2f6aaefb0
https://github.com/galaxyproject/galaxy/commit/20565a2b8517fbc4c54524fa0ae1…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-11 (Wed, 11 Jul 2018)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
Log Message:
-----------
Merge pull request #6375 from dannon/sentry_transport_fix
[18.05] Specify standard HTTPTransport for Sentry
Commit: dfc996c8d6b8e166ae17fe8502f9e4f9252b6106
https://github.com/galaxyproject/galaxy/commit/dfc996c8d6b8e166ae17fe8502f9…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-07-13 (Fri, 13 Jul 2018)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Merge branch 'release_18.01' into release_18.05
Commit: 2abb01b6cbb11f28a7f6a838c97b8540b62e45fb
https://github.com/galaxyproject/galaxy/commit/2abb01b6cbb11f28a7f6a838c97b…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-07-13 (Fri, 13 Jul 2018)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/web/base/controller.py
Log Message:
-----------
Merge branch 'release_18.05' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/fa43f2c2b2e7...2abb01b6cbb1
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b0693203a1ed4d755f6fac261dd98bdddb6da6b2
https://github.com/galaxyproject/galaxy/commit/b0693203a1ed4d755f6fac261dd9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M lib/galaxy/managers/tags.py
Log Message:
-----------
Allow : in tag values for PJA setting.
Based on #5457, certain paths to creating tag values with : must already work - just not when parsing from a raw string I guess.
Commit: b45ce119401b6ef36a19c1bd21c84856ebc074e2
https://github.com/galaxyproject/galaxy/commit/b45ce119401b6ef36a19c1bd21c8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/actions/__init__.py
Log Message:
-----------
Centralize logic for determining which tags get auto-propagated.
Commit: 0280713c43442a412cf6294b57caf1c12160322f
https://github.com/galaxyproject/galaxy/commit/0280713c43442a412cf6294b57ca…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M lib/galaxy/model/__init__.py
M test/api/test_workflows.py
Log Message:
-----------
Auto-propagate group tags - the way name tags are propagated.
Commit: 2cccf7c23fc57e4e633af2b1703d7d4a034f5850
https://github.com/galaxyproject/galaxy/commit/2cccf7c23fc57e4e633af2b1703d…
Author: Nicola Soranzo <nicola.soranzo(a)gmail.com>
Date: 2018-07-12 (Thu, 12 Jul 2018)
Changed paths:
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/__init__.py
M lib/galaxy/tools/actions/__init__.py
M test/api/test_workflows.py
Log Message:
-----------
Merge pull request #6491 from jmchilton/auto_group_tags
Implement ``group:`` tags (toward multi-factor analysis with group tagging)
Compare: https://github.com/galaxyproject/galaxy/compare/0674af824d2c...2cccf7c23fc5
**NOTE:** This service been marked for deprecation: https://developer.github.com/changes/2018-04-25-github-services-deprecation/
Functionality will be removed from GitHub.com on January 31st, 2019.