Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 68240630668848b454aa51690ed1ac7bbfbc16e2
https://github.com/galaxyproject/galaxy/commit/68240630668848b454aa51690ed1…
Author: chambm <matt.chambers42(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/tool_shed/util/common_util.py
Log Message:
-----------
* Fix get_latest_installable_revision to use pathspec and params to work with recent changes to common_util.url_join
* Fix common_util.url_join to handle a string as pathspec, instead of treating it as an a/r/r/a/y/ /o/f/ /c/h/a/r/a/c/t/e/r/s
Commit: d375a8cc034acaea43e221cb60fe58ece5f5d4d6
https://github.com/galaxyproject/galaxy/commit/d375a8cc034acaea43e221cb60fe…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/tool_shed/util/common_util.py
Log Message:
-----------
Merge pull request #632 from chambm/bug/url_join-latest_revision-2
Cleaner commit history for #629 and array syntax for pathspec
Compare: https://github.com/galaxyproject/galaxy/compare/eb59844dd2fa...d375a8cc034a
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 0930035a9f5629836702525822095daf598dce45
https://github.com/galaxyproject/galaxy/commit/0930035a9f562983670252582209…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-20 (Thu, 20 Aug 2015)
Changed paths:
M templates/spark_base.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
Log Message:
-----------
Fixed bug where max items per page was reset when changing the
amount of time sparklines spanned
Commit: 673dd2b140791fade4c2943abc399d718b789950
https://github.com/galaxyproject/galaxy/commit/673dd2b140791fade4c2943abc39…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-20 (Thu, 20 Aug 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/reports_webapp/run_stats.js
M templates/base.mako
Log Message:
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Refactored where d3 is coming from
Commit: 78251936e8df0256828f22130c42922190800ecc
https://github.com/galaxyproject/galaxy/commit/78251936e8df0256828f22130c42…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-20 (Thu, 20 Aug 2015)
Changed paths:
M templates/base.mako
M templates/webapps/reports/run_stats.mako
Log Message:
-----------
Moved d3 import to run_stats
Commit: 963d3fe6591a19c3940daeb20c13a5c4566653ad
https://github.com/galaxyproject/galaxy/commit/963d3fe6591a19c3940daeb20c13…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
Log Message:
-----------
Fixed bug where column sorting reset paging info
Commit: 245a3ccd9ef5c37f45529c69f3802b7269025333
https://github.com/galaxyproject/galaxy/commit/245a3ccd9ef5c37f45529c69f380…
Author: Airistotal <danieltos.bouchard(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M templates/webapps/reports/run_stats.mako
Log Message:
-----------
Fixed error on homepage
Commit: eb59844dd2fa28734fb0ce3a051d582e2eac723f
https://github.com/galaxyproject/galaxy/commit/eb59844dd2fa28734fb0ce3a051d…
Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M client/galaxy/scripts/reports_webapp/run_stats.js
M static/maps/reports_webapp/run_stats.js.map
M static/scripts/reports_webapp/run_stats.js
M templates/base.mako
M templates/spark_base.mako
M templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/run_stats.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_per_workflow.mako
Log Message:
-----------
Merge pull request #626 from Airistotal/dev
Bug fix in Reports
Compare: https://github.com/galaxyproject/galaxy/compare/950f471c2326...eb59844dd2fa
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: a3e511292afe6dcdbb3bf533ef6b6e2520c2c652
https://github.com/galaxyproject/galaxy/commit/a3e511292afe6dcdbb3bf533ef6b…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-08-12 (Wed, 12 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/form/form-select-content.js
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M static/maps/mvc/form/form-select-content.js.map
M static/scripts/mvc/form/form-select-content.js
Log Message:
-----------
Merge branch 'release_15.05'
Commit: a8a1a150c6ec1a474753052b96b25aec8a22813e
https://github.com/galaxyproject/galaxy/commit/a8a1a150c6ec1a474753052b96b2…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-08-12 (Wed, 12 Aug 2015)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Merge branch 'release_15.05'
Commit: 130004feb10f1fe3a26908401146b8e47c1202ff
https://github.com/galaxyproject/galaxy/commit/130004feb10f1fe3a26908401146…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2015-08-12 (Wed, 12 Aug 2015)
Changed paths:
M .ci/flake8_wrapper.sh
M .ci/pep8_sources.txt
M .gitignore
M CONTRIBUTING.md
A CONTRIBUTORS.md
M LICENSE.txt
M README.rst
M client/GruntFile.js
M client/README.md
M client/bower.json
R client/galaxy/scripts/galaxy.workflow_editor.canvas.js
R client/galaxy/scripts/galaxy.workflows.js
M client/galaxy/scripts/libs/d3.js
M client/galaxy/scripts/libs/jquery/jquery.js
M client/galaxy/scripts/libs/raven.js
M client/galaxy/scripts/libs/require.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/library/library-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/tools/tools-form-base.js
M client/galaxy/scripts/mvc/tools/tools-form-workflow.js
A client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
A client/galaxy/scripts/mvc/ui/ui-select-ftp.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
A client/galaxy/scripts/mvc/workflow/workflow-canvas.js
A client/galaxy/scripts/mvc/workflow/workflow-connector.js
A client/galaxy/scripts/mvc/workflow/workflow-manager.js
A client/galaxy/scripts/mvc/workflow/workflow-node.js
A client/galaxy/scripts/mvc/workflow/workflow-terminals.js
A client/galaxy/scripts/mvc/workflow/workflow-view-data.js
A client/galaxy/scripts/mvc/workflow/workflow-view-node.js
A client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
A client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/trackster/tracks.js
A client/galaxy/style/blue_colors.ini
A client/galaxy/style/less/autocomplete_tagging.less
A client/galaxy/style/less/base.less
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A client/galaxy/style/less/bootstrap/alerts.less
A client/galaxy/style/less/bootstrap/badges.less
A client/galaxy/style/less/bootstrap/bootstrap.less
A client/galaxy/style/less/bootstrap/breadcrumbs.less
A client/galaxy/style/less/bootstrap/button-groups.less
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A client/galaxy/style/less/bootstrap/close.less
A client/galaxy/style/less/bootstrap/code.less
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A client/galaxy/style/less/bootstrap/grid.less
A client/galaxy/style/less/bootstrap/input-groups.less
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A client/galaxy/style/less/bootstrap/modals.less
A client/galaxy/style/less/bootstrap/navbar.less
A client/galaxy/style/less/bootstrap/navs.less
A client/galaxy/style/less/bootstrap/normalize.less
A client/galaxy/style/less/bootstrap/pager.less
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A client/galaxy/style/less/bootstrap/panels.less
A client/galaxy/style/less/bootstrap/popovers.less
A client/galaxy/style/less/bootstrap/print.less
A client/galaxy/style/less/bootstrap/progress-bars.less
A client/galaxy/style/less/bootstrap/responsive-utilities.less
A client/galaxy/style/less/bootstrap/scaffolding.less
A client/galaxy/style/less/bootstrap/tables.less
A client/galaxy/style/less/bootstrap/theme.less
A client/galaxy/style/less/bootstrap/thumbnails.less
A client/galaxy/style/less/bootstrap/tooltip.less
A client/galaxy/style/less/bootstrap/type.less
A client/galaxy/style/less/bootstrap/utilities.less
A client/galaxy/style/less/bootstrap/variables.less
A client/galaxy/style/less/bootstrap/wells.less
A client/galaxy/style/less/circster.less
A client/galaxy/style/less/collections.less
A client/galaxy/style/less/embed_item.less
A client/galaxy/style/less/fontawesome/bordered-pulled.less
A client/galaxy/style/less/fontawesome/core.less
A client/galaxy/style/less/fontawesome/fixed-width.less
A client/galaxy/style/less/fontawesome/font-awesome.less
A client/galaxy/style/less/fontawesome/icons.less
A client/galaxy/style/less/fontawesome/larger.less
A client/galaxy/style/less/fontawesome/list.less
A client/galaxy/style/less/fontawesome/mixins.less
A client/galaxy/style/less/fontawesome/path.less
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A client/galaxy/style/less/fontawesome/spinning.less
A client/galaxy/style/less/fontawesome/stacked.less
A client/galaxy/style/less/fontawesome/variables.less
A client/galaxy/style/less/frame.less
A client/galaxy/style/less/galaxy_bootstrap.less
A client/galaxy/style/less/galaxy_bootstrap/overrides.less
A client/galaxy/style/less/galaxy_bootstrap/variables.less
A client/galaxy/style/less/galaxy_variables.less
A client/galaxy/style/less/history.less
A client/galaxy/style/less/iconic_stroke.less
A client/galaxy/style/less/iphone.less
A client/galaxy/style/less/job.less
A client/galaxy/style/less/jstree.less
A client/galaxy/style/less/library.less
A client/galaxy/style/less/list-item.less
A client/galaxy/style/less/masthead.less
A client/galaxy/style/less/select2.less
A client/galaxy/style/less/theme/blue.less
A client/galaxy/style/less/toastr.less
A client/galaxy/style/less/trackster.less
A client/galaxy/style/less/ui.less
A client/galaxy/style/less/ui/dataset-choice.less
A client/galaxy/style/less/ui/icon-btn.less
A client/galaxy/style/less/ui/pagination.less
A client/galaxy/style/less/ui/paired-collection-creator.less
A client/galaxy/style/less/ui/peek-column-selector.less
A client/galaxy/style/less/ui/search-input.less
A client/galaxy/style/less/upload.less
A client/galaxy/style/source_material/circle.py
A client/galaxy/style/source_material/galaxy_icons.svg
A client/galaxy/style/source_material/galaxy_spinner.fla
A client/grunt-tasks/install-libs.js
A client/grunt-tasks/scripts.js
A client/grunt-tasks/style.js
M client/package.json
A client/toolshed/scripts/mvc/groups/group-detail-view.js
A client/toolshed/scripts/mvc/groups/group-list-view.js
A client/toolshed/scripts/mvc/groups/group-listrow-view.js
A client/toolshed/scripts/mvc/groups/group-model.js
A client/toolshed/scripts/toolshed.groups.js
M config/auth_conf.xml.sample
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M config/job_conf.xml.sample_advanced
M config/object_store_conf.xml.sample
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ipython/config/ipython.ini.sample
M config/plugins/interactive_environments/ipython/config/ipython.xml
M config/plugins/interactive_environments/ipython/templates/ipython.mako
M config/plugins/interactive_environments/ipython/templates/notebook.ipynb
A config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample
A config/plugins/interactive_environments/rstudio/config/rstudio.xml
A config/plugins/interactive_environments/rstudio/static/js/crypto/base64.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/jsbn.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/prng4.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rng.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rsa.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.big.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio.min.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/base64.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/jsbn.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/prng4.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rng.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/rstudio/rsa.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/base64.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/jsbn.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/prng4.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rng.js
A config/plugins/interactive_environments/rstudio/static/js/crypto/wu/rsa.js
A config/plugins/interactive_environments/rstudio/static/js/rstudio.js
A config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/visualizations/README.txt
M config/plugins/visualizations/charts/config/charts.xml
M config/plugins/visualizations/charts/templates/charts.mako
M config/plugins/visualizations/circster/config/circster.xml
M config/plugins/visualizations/common/templates/visualization_base.mako
M config/plugins/visualizations/graphview/config/graphview.xml
M config/plugins/visualizations/phyloviz/config/phyloviz.xml
M config/plugins/visualizations/scatterplot/config/scatterplot.xml
M config/plugins/visualizations/scatterplot/src/scatterplot-display.js
M config/plugins/visualizations/scatterplot/static/scatterplot-edit.js
M config/plugins/visualizations/sweepster/config/sweepster.xml
M config/plugins/visualizations/trackster/config/trackster.xml
M config/plugins/visualizations/visualization.dtd
M config/tool_conf.xml.sample
M config/tool_shed.ini.sample
M cron/parse_builds.py
M display_applications/ensembl/ensembl_bam.xml
M display_applications/ensembl/ensembl_gff.xml
M display_applications/ensembl/ensembl_interval_as_bed.xml
M display_applications/gbrowse/gbrowse_gff.xml
M display_applications/gbrowse/gbrowse_interval_as_bed.xml
M display_applications/gbrowse/gbrowse_wig.xml
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
M display_applications/igv/bam.xml
M display_applications/igv/gff.xml
A display_applications/igv/interval_as_bed.xml
M display_applications/igv/vcf.xml
M display_applications/rviewer/bed.xml
M display_applications/rviewer/vcf.xml
A doc/source/api_doc.rst
M doc/source/conf.py
M doc/source/index.rst
R doc/source/lib/fpconst.rst
M doc/source/lib/galaxy.actions.rst
A doc/source/lib/galaxy.auth.providers.rst
A doc/source/lib/galaxy.auth.rst
A doc/source/lib/galaxy.dataset_collections.rst
A doc/source/lib/galaxy.dataset_collections.types.rst
M doc/source/lib/galaxy.datatypes.converters.rst
A 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.eggs.rst
M doc/source/lib/galaxy.exceptions.rst
M doc/source/lib/galaxy.external_services.result_handlers.rst
M doc/source/lib/galaxy.external_services.rst
M doc/source/lib/galaxy.forms.rst
M doc/source/lib/galaxy.jobs.actions.rst
M doc/source/lib/galaxy.jobs.deferred.rst
A doc/source/lib/galaxy.jobs.metrics.collectl.rst
A doc/source/lib/galaxy.jobs.metrics.instrumenters.rst
A doc/source/lib/galaxy.jobs.metrics.rst
M doc/source/lib/galaxy.jobs.rst
R doc/source/lib/galaxy.jobs.runners.cli_job.rst
R doc/source/lib/galaxy.jobs.runners.cli_shell.rst
A doc/source/lib/galaxy.jobs.runners.lwr_client.rst
A doc/source/lib/galaxy.jobs.runners.lwr_client.staging.rst
A doc/source/lib/galaxy.jobs.runners.lwr_client.transport.rst
M doc/source/lib/galaxy.jobs.runners.rst
A doc/source/lib/galaxy.jobs.runners.state_handlers.rst
A doc/source/lib/galaxy.jobs.runners.util.cli.job.rst
A doc/source/lib/galaxy.jobs.runners.util.cli.rst
A doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst
A doc/source/lib/galaxy.jobs.runners.util.condor.rst
A doc/source/lib/galaxy.jobs.runners.util.job_script.rst
A doc/source/lib/galaxy.jobs.runners.util.rst
M doc/source/lib/galaxy.jobs.splitters.rst
M doc/source/lib/galaxy.managers.rst
M doc/source/lib/galaxy.model.migrate.rst
R doc/source/lib/galaxy.model.orm.ext.rst
M doc/source/lib/galaxy.model.orm.rst
M doc/source/lib/galaxy.model.rst
A doc/source/lib/galaxy.model.tool_shed_install.migrate.rst
A doc/source/lib/galaxy.model.tool_shed_install.rst
M doc/source/lib/galaxy.objectstore.rst
M doc/source/lib/galaxy.openid.rst
M doc/source/lib/galaxy.quota.rst
M doc/source/lib/galaxy.rst
M doc/source/lib/galaxy.sample_tracking.rst
M doc/source/lib/galaxy.security.rst
M doc/source/lib/galaxy.tags.rst
R doc/source/lib/galaxy.tool_shed.migrate.rst
R doc/source/lib/galaxy.tool_shed.rst
R doc/source/lib/galaxy.tool_shed.tool_dependencies.rst
M doc/source/lib/galaxy.tools.actions.rst
M doc/source/lib/galaxy.tools.data.rst
A doc/source/lib/galaxy.tools.data_manager.rst
A doc/source/lib/galaxy.tools.deps.resolvers.rst
M doc/source/lib/galaxy.tools.deps.rst
A doc/source/lib/galaxy.tools.filters.rst
R doc/source/lib/galaxy.tools.genome_index.rst
M doc/source/lib/galaxy.tools.imp_exp.rst
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A doc/source/lib/galaxy.tools.parser.rst
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A doc/source/lib/galaxy.tools.toolbox.filters.rst
A doc/source/lib/galaxy.tools.toolbox.lineages.rst
A doc/source/lib/galaxy.tools.toolbox.rst
M doc/source/lib/galaxy.tools.util.galaxyops.rst
M doc/source/lib/galaxy.tools.util.rst
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M doc/source/lib/galaxy.util.rst
M doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst
M doc/source/lib/galaxy.visualization.data_providers.rst
M doc/source/lib/galaxy.visualization.genome.rst
A doc/source/lib/galaxy.visualization.plugins.rst
M doc/source/lib/galaxy.visualization.rst
M doc/source/lib/galaxy.visualization.tracks.rst
M doc/source/lib/galaxy.web.base.controllers.rst
M doc/source/lib/galaxy.web.base.rst
M doc/source/lib/galaxy.web.framework.helpers.rst
M doc/source/lib/galaxy.web.framework.middleware.rst
M doc/source/lib/galaxy.web.framework.rst
A doc/source/lib/galaxy.web.proxy.rst
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R doc/source/lib/galaxy.webapps.community.framework.rst
R doc/source/lib/galaxy.webapps.community.model.migrate.rst
R doc/source/lib/galaxy.webapps.community.model.rst
R doc/source/lib/galaxy.webapps.community.rst
R doc/source/lib/galaxy.webapps.community.security.rst
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M doc/source/lib/galaxy.webapps.galaxy.rst
M doc/source/lib/galaxy.webapps.reports.controllers.rst
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M doc/source/lib/galaxy.webapps.tool_shed.framework.rst
M doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst
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M doc/source/lib/psyco_full.rst
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A doc/source/lib/pulsar.client.transport.rst
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A doc/source/lib/tool_shed.dependencies.rst
A doc/source/lib/tool_shed.dependencies.tool.rst
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M doc/source/releases/15.05.rst
A doc/source/releases/15.07_announce.rst
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M lib/galaxy/app.py
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A lib/galaxy/auth/providers/pam_auth.py
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M lib/galaxy/datatypes/chrominfo.py
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A lib/galaxy/datatypes/proteomics.py
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M lib/galaxy/managers/histories.py
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M lib/galaxy/model/__init__.py
M lib/galaxy/model/search.py
M lib/galaxy/objectstore/__init__.py
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M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
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M lib/galaxy/tools/actions/data_source.py
M lib/galaxy/tools/actions/history_imp_exp.py
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M lib/galaxy/tools/actions/upload_common.py
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M lib/galaxy/tools/loader.py
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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/input_translation.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
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M lib/galaxy/tools/util/galaxyops/__init__.py
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M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/streamball.py
A lib/galaxy/util/xml_macros.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/registry.py
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A lib/galaxy/visualization/plugins/plugin.py
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A lib/galaxy/visualization/plugins/resource_parser.py
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R lib/galaxy/visualization/registry.py
M lib/galaxy/web/base/controllers/admin.py
M lib/galaxy/web/base/interactive_environments.py
M lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/js/lib/proxy.js
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
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M lib/galaxy/webapps/galaxy/api/workflows.py
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M lib/galaxy/webapps/galaxy/controllers/dataset.py
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M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/userskeys.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
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M lib/galaxy/workflow/steps.py
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M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
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M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/cleanup_datasets/populate_uuid.py
M scripts/cleanup_datasets/remove_renamed_datasets_from_disk.py
M scripts/cleanup_datasets/rename_purged_datasets.py
M scripts/cleanup_datasets/update_dataset_size.py
M scripts/cleanup_datasets/update_metadata.py
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A scripts/edam_mapping.py
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A scripts/runtime_stats.py
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M static/maps/libs/jquery/jquery.js.map
M static/maps/libs/require.js.map
M static/maps/mvc/collection/collection-model.js.map
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M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/form/form-data.js
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M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/library/library-folderlist-view.js
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M static/scripts/mvc/library/library-foldertoolbar-view.js
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M static/scripts/mvc/ui/ui-select-default.js
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M static/scripts/utils/utils.js
M static/scripts/viz/trackster/tracks.js
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R static/style/README
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R static/style/blue_colors.ini
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R static/style/src/less/autocomplete_tagging.less
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A templates/admin/tool_errors.mako
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M templates/webapps/galaxy/workflow/run.mako
M templates/webapps/reports/index.mako
A templates/webapps/reports/jobs_errors_per_tool.mako
M templates/webapps/reports/jobs_per_month_all.mako
M templates/webapps/reports/jobs_per_month_in_error.mako
M templates/webapps/reports/jobs_per_tool.mako
M templates/webapps/reports/jobs_per_user.mako
M templates/webapps/reports/jobs_specified_month_all.mako
M templates/webapps/reports/jobs_specified_month_in_error.mako
M templates/webapps/reports/jobs_tool_per_month.mako
M templates/webapps/reports/jobs_user_per_month.mako
M templates/webapps/reports/registered_users.mako
M templates/webapps/reports/registered_users_per_month.mako
M templates/webapps/reports/requests_user_per_month.mako
M templates/webapps/reports/users_last_access_date.mako
M templates/webapps/reports/users_user_disk_usage.mako
M templates/webapps/reports/workflows_per_month_all.mako
M templates/webapps/reports/workflows_per_user.mako
M templates/webapps/reports/workflows_user_per_month.mako
M templates/webapps/tool_shed/base_panels.mako
A templates/webapps/tool_shed/group/index.mako
M templates/webapps/tool_shed/repository/common.mako
M templates/webapps/tool_shed/repository/manage_repository.mako
M templates/webapps/tool_shed/repository/view_repository.mako
A test-data/bcf_index_metadata_test.bcf
A test-data/bcf_index_metadata_test.txt
M test/api/test_tools.py
M test/base/twilltestcase.py
M test/functional/test_toolbox.py
A test/functional/tool-data/fasta_indexes.loc
M test/functional/tool-data/sample_tool_data_tables.xml
M test/functional/tools/code_file.py
A test/functional/tools/dbkey_filter_input.xml
A test/functional/tools/dbkey_filter_multi_input.xml
A test/functional/tools/environment_variables.xml
A test/functional/tools/library_data.xml
A test/functional/tools/metadata_bcf.xml
A test/functional/tools/output_collection_filter.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/install_and_test_tool_shed_repositories/base/util.py
M test/qunit/test-common.js
M test/qunit/tests/workflow_editor_tests.js
M test/unit/jobs/test_job_configuration.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/tool_shed_unit_tests/test_td_common_util.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_tool_dependency_description.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/unittest_utils/galaxy_mock.py
A test/unit/visualizations/plugins/__init__.py
A test/unit/visualizations/plugins/test_VisualizationPlugin.py
A test/unit/visualizations/plugins/test_VisualizationsRegistry.py
R test/unit/visualizations/test_VisualizationsRegistry.py
M tools/data_source/bed_convert.xml
M tools/data_source/genbank.xml
M tools/data_source/import.xml
M tools/data_source/microbial_import.xml
M tools/data_source/ucsc_tablebrowser_archaea.xml
M tools/data_source/ucsc_tablebrowser_test.xml
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/codingSnps.xml
M tools/evolution/codingSnps_filter.py
M tools/extract/liftOver_wrapper.xml
M tools/filters/axt_to_lav.xml
M tools/filters/axt_to_lav_code.py
M tools/filters/catWrapper.xml
M tools/filters/changeCase.xml
M tools/filters/condense_characters.xml
M tools/filters/cutWrapper.xml
M tools/filters/gff/extract_GFF_Features.xml
M tools/filters/gff/gff_filter_by_attribute.xml
M tools/filters/gff/gff_filter_by_feature_count.xml
M tools/filters/gff/gtf_filter_by_attribute_values_list.xml
M tools/filters/headWrapper.xml
M tools/filters/joiner2.xml
M tools/filters/lav_to_bed.py
M tools/filters/lav_to_bed.xml
M tools/filters/lav_to_bed_code.py
M tools/filters/pasteWrapper.xml
M tools/filters/remove_beginning.xml
M tools/filters/tailWrapper.xml
M tools/filters/ucsc_gene_table_to_intervals.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/maf_by_block_number.xml
M tools/maf/maf_filter.py
M tools/maf/maf_filter.xml
M tools/maf/maf_limit_size.xml
M tools/maf/maf_reverse_complement.py
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_to_fasta.xml
M tools/plotting/bar_chart.xml
M tools/plotting/boxplot.xml
M tools/solid_tools/maq_cs_wrapper_code.py
M tools/stats/filtering.xml
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tools/stats/gsummary.xml
M tools/stats/gsummary.xml.groups
M tools/visualization/LAJ.xml
M tools/visualization/LAJ_code.py
Log Message:
-----------
Merge branch 'release_15.07'
Commit: 737248d41d4e1d682361b85d48ea65574367e59d
https://github.com/galaxyproject/galaxy/commit/737248d41d4e1d682361b85d48ea…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-20 (Thu, 20 Aug 2015)
Changed paths:
M lib/galaxy/workflow/render.py
Log Message:
-----------
Fix for valid height/width definitions in workflow rendering code.
Commit: b8fd98979c775daf46a768572fb30f4467fd7458
https://github.com/galaxyproject/galaxy/commit/b8fd98979c775daf46a768572fb3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-20 (Thu, 20 Aug 2015)
Changed paths:
M lib/galaxy/workflow/render.py
Log Message:
-----------
Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings.
Commit: 083789526105abda87a701835b8ff44e0ec89405
https://github.com/galaxyproject/galaxy/commit/083789526105abda87a701835b8f…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M lib/galaxy/workflow/render.py
Log Message:
-----------
Merge pull request #625 from dannon/release_15.07
[release_15.07] Fix for valid height/width definitions in workflow rendering code, and fix identifiers.
Commit: b29e81014979d2e72d704a22560a278cfec42927
https://github.com/galaxyproject/galaxy/commit/b29e81014979d2e72d704a22560a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M lib/galaxy/workflow/render.py
Log Message:
-----------
Fix for valid height/width definitions in workflow rendering code.
Commit: 4d2651a085405f2b4ba37f26fa917f9524584b1a
https://github.com/galaxyproject/galaxy/commit/4d2651a085405f2b4ba37f26fa91…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M lib/galaxy/workflow/render.py
Log Message:
-----------
Fix the second (and final) issue preventing workflow rendering from generating valid SVGs -- incorrect usage of arrow_end; this is intended to be a unique identifier for the element and not a boolean. This wasn't preventing render (on firefox or chrome) like the previous issue, but it would cause warnings.
Commit: e06d6a1ccae792abb45ff96d63bf8ab51e685231
https://github.com/galaxyproject/galaxy/commit/e06d6a1ccae792abb45ff96d63bf…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M lib/galaxy/workflow/render.py
Log Message:
-----------
Merge branch 'release_15.01' into release_15.03
Commit: c569f7856d41fe9b51808302569283c800a4eb93
https://github.com/galaxyproject/galaxy/commit/c569f7856d41fe9b518083025692…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M lib/galaxy/workflow/render.py
Log Message:
-----------
Merge branch 'release_15.03' into release_15.05
Commit: e8f90429e2ca3efc6dbb9f02b1d5fbe8afc446a5
https://github.com/galaxyproject/galaxy/commit/e8f90429e2ca3efc6dbb9f02b1d5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Log Message:
-----------
Merge branch 'release_15.05' into release_15.07
Commit: d055102596d85b5a3d6da90e8397016f6daf2271
https://github.com/galaxyproject/galaxy/commit/d055102596d85b5a3d6da90e8397…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M lib/galaxy/model/__init__.py
M lib/galaxy/webapps/galaxy/api/tools.py
M lib/galaxy/workflow/render.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M scripts/cleanup_datasets/cleanup_datasets.py
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/scripts/mvc/workflow/workflow-terminals.js
M test/unit/test_galaxy_mapping.py
Log Message:
-----------
Merge branch 'release_15.07'
Commit: 950f471c2326cc8d90c7efe372c063f47ed7f3e4
https://github.com/galaxyproject/galaxy/commit/950f471c2326cc8d90c7efe372c0…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2015-08-21 (Fri, 21 Aug 2015)
Changed paths:
M lib/galaxy/workflow/render.py
Log Message:
-----------
Merge branch 'master' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/795e30171149...950f471c2326