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- 15302 discussions
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: e8b78cb62b187c0119440f91f0c43a4bfc86aa2d
https://github.com/galaxyproject/galaxy/commit/e8b78cb62b187c0119440f91f0c4…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M scripts/migrate_tools/migrate_tools.py
Log Message:
-----------
Fix typos
Commit: 24d2d3b4fa543b20f8454e7e2e55ad78c72fdc28
https://github.com/galaxyproject/galaxy/commit/24d2d3b4fa543b20f8454e7e2e55…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Print toolbox dict if test fails
Commit: eec60eef19439a7d4b51a75602bc8d3e49c8afde
https://github.com/galaxyproject/galaxy/commit/eec60eef19439a7d4b51a75602bc…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M lib/galaxy/managers/containers.py
Log Message:
-----------
Remove unused class
Commit: b281611e2631ac46a51066a09add94def4126988
https://github.com/galaxyproject/galaxy/commit/b281611e2631ac46a51066a09add…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Compile but not exec code files on TS submission
Commit: 7909b90e9438042fc2a9032763f3f851ffdad433
https://github.com/galaxyproject/galaxy/commit/7909b90e9438042fc2a9032763f3…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M lib/galaxy/web/framework/webapp.py
Log Message:
-----------
Remove unneeded encode()
`GalaxySession.session_key` is of type `TrimmedString(255)`, which is
implemented using `sqlalchemy.types.String` and should accept Unicode
objects.
Commit: 3aa7af6372e76cd1ed34b1c21f327cc87b07241c
https://github.com/galaxyproject/galaxy/commit/3aa7af6372e76cd1ed34b1c21f32…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M lib/galaxy/managers/containers.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/web/framework/webapp.py
M scripts/migrate_tools/migrate_tools.py
M test/unit/tools/test_toolbox.py
Log Message:
-----------
Merge pull request #5638 from nsoranzo/misc
Small misc fixes and cleanups
Compare: https://github.com/galaxyproject/galaxy/compare/7adb60fdbeab...3aa7af6372e7
1
0
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: a6593d4cafe966062460e33eaac1c5a28566c109
https://github.com/galaxyproject/galaxy/commit/a6593d4cafe966062460e33eaac1…
Author: Matthias Bernt <m.bernt(a)ufz.de>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M tools/stats/gsummary.py
Log Message:
-----------
python3 fix
strings can not be written to byte mode file handlers.
writing resulted in:
TypeError: a bytes-like object is required, not 'str'
Alternative would be to make string byte.
Commit: 28724ab795ac5dfcc5fa5b9a9a88fb0b64fc7752
https://github.com/galaxyproject/galaxy/commit/28724ab795ac5dfcc5fa5b9a9a88…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-03-05 (Mon, 05 Mar 2018)
Changed paths:
M tools/stats/gsummary.py
Log Message:
-----------
Merge pull request #5639 from nsoranzo/release_17.09_backport_5043
[17.09] Backport of #5043
Compare: https://github.com/galaxyproject/galaxy/compare/2d132a45d9af...28724ab795ac
1
0
05 Mar '18
Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: bd69278f0bcc67afc1eb827a8a7bc80ae7766072
https://github.com/galaxyproject/galaxy/commit/bd69278f0bcc67afc1eb827a8a7b…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M test/functional/tools/multi_output_recurse.xml
Log Message:
-----------
Add a testcase for optional output discovery
This test correctly fails with:
```
galaxy.jobs.runners.local ERROR 2018-03-02 17:55:32,396 Job wrapper finish method failed
Traceback (most recent call last):
File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/local.py", line 152, in queue_job
self._finish_or_resubmit_job(job_state, stdout, stderr, exit_code)
File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/runners/__init__.py", line 432, in _finish_or_resubmit_job
job_state.job_wrapper.finish(stdout, stderr, exit_code, check_output_detected_state=check_output_detected_state)
File "/Users/mvandenb/src/galaxy/lib/galaxy/jobs/__init__.py", line 1381, in finish
'primary': self.tool.collect_primary_datasets(out_data, self.get_tool_provided_job_metadata(), tool_working_directory, input_ext, input_dbkey)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/__init__.py", line 1614, in collect_primary_datasets
return output_collect.collect_primary_datasets(self, output, tool_provided_metadata, job_working_directory, input_ext, input_dbkey=input_dbkey)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 372, in collect_primary_datasets
for discovered_file in discover_files(name, tool_provided_metadata, dataset_collectors, job_working_directory, outdata):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 490, in discover_files
for (match, collector) in walk_over_file_collectors(extra_file_collectors, job_working_directory, matchable):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 507, in walk_over_file_collectors
for match in walk_over_extra_files(extra_file_collector.directory, extra_file_collector, job_working_directory, matchable):
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/parameters/output_collect.py", line 519, in walk_over_extra_files
for filename in os.listdir(directory):
OSError: [Errno 2] No such file or directory: '/private/var/folders/df/6xqpqpcd7h73b6jpx9t6cwhw0000gn/T/tmp5Tz0m9/tmpfUHHl6/tmpVBcnfI/database/job_working_directory_LJioiW/000/2/working/i_do_not_exist'
```
Commit: d21d7d9d2e10d9c09bdbadbf328fd3eef84630e6
https://github.com/galaxyproject/galaxy/commit/d21d7d9d2e10d9c09bdbadbf328f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/output_collect.py
Log Message:
-----------
Fix output discovery when directory doesn't exist
This broke in 8b76a5a698fd3bc13d4acc38194221def9ed5163.
Checking if `directory` is a directory is what we had done previously.
Commit: 7ed81e18101c33a1e83bb5e72851698910a118e9
https://github.com/galaxyproject/galaxy/commit/7ed81e18101c33a1e83bb5e72851…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M test/functional/tools/multi_output_recurse.xml
Log Message:
-----------
Move `optional` tag to the output data element
Thx @nsoranzo!
Commit: da867852ae6437c02c64287521dde0b8aa1e8109
https://github.com/galaxyproject/galaxy/commit/da867852ae6437c02c64287521dd…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M test/functional/tools/multi_output_recurse.xml
Log Message:
-----------
Drop optional="true" altogther
Commit: d77845268a9243535e2b77383bc4ed3d433e2e7a
https://github.com/galaxyproject/galaxy/commit/d77845268a9243535e2b77383bc4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-04 (Sun, 04 Mar 2018)
Changed paths:
M lib/galaxy/tools/parameters/output_collect.py
M test/functional/tools/multi_output_recurse.xml
Log Message:
-----------
Merge pull request #5635 from mvdbeek/fix_optional_output_discovery
[18.01] Fix output discovery if dir doesn't exist
Compare: https://github.com/galaxyproject/galaxy/compare/e01f9fa1b89e...d77845268a92
1
0
05 Mar '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 99c377e59a3191a2161a5b769571aed8474ffdc3
https://github.com/galaxyproject/galaxy/commit/99c377e59a3191a2161a5b769571…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/lmod.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/monitors.py
M lib/galaxy/util/none_like.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/reports/controllers/query.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Use new style classes for Py2/3 consistency
Also small import refactoring in `lib/galaxy/tools/deps/resolvers/` .
Commit: 7adb60fdbeabad91cfb68a621d20726f916388d7
https://github.com/galaxyproject/galaxy/commit/7adb60fdbeabad91cfb68a621d20…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-04 (Sun, 04 Mar 2018)
Changed paths:
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/exceptions/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/container_resolvers/__init__.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/brewed_tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/deps/resolvers/homebrew.py
M lib/galaxy/tools/deps/resolvers/lmod.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/util/inflection.py
M lib/galaxy/util/monitors.py
M lib/galaxy/util/none_like.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/base/controller.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/reports/controllers/query.py
M lib/galaxy/webapps/tool_shed/security/__init__.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Merge pull request #5636 from nsoranzo/new_style_classes
Use new style classes for Py2/3 consistency
Compare: https://github.com/galaxyproject/galaxy/compare/0e0e8e9bd6d4...7adb60fdbeab
1
0
02 Mar '18
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b0b3f5f12f16adec7d68015d86ef827976378105
https://github.com/galaxyproject/galaxy/commit/b0b3f5f12f16adec7d68015d86ef…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2018-02-23 (Fri, 23 Feb 2018)
Changed paths:
M lib/galaxy/util/path/__init__.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
Log Message:
-----------
allows whitelisted symlinks to be imported from
needs testing
Commit: 340d4b7b3f365d8fb0a1d6d19347322cfb3bdd9d
https://github.com/galaxyproject/galaxy/commit/340d4b7b3f365d8fb0a1d6d19347…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2018-02-23 (Fri, 23 Feb 2018)
Changed paths:
M lib/galaxy/util/path/__init__.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
Log Message:
-----------
comment whitespace fixes
Commit: e4d259e0c647e699c15e71ff8c43910e775752ed
https://github.com/galaxyproject/galaxy/commit/e4d259e0c647e699c15e71ff8c43…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-02-26 (Mon, 26 Feb 2018)
Changed paths:
M lib/galaxy/util/path/__init__.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
Log Message:
-----------
A couple additions to @bwlang's whitelist additions for the remote_files
API.
Commit: a01747054202d2cb843c3280f0361bfa34219e2a
https://github.com/galaxyproject/galaxy/commit/a01747054202d2cb843c3280f036…
Author: Brad Langhorst <langhorst(a)neb.com>
Date: 2018-02-26 (Mon, 26 Feb 2018)
Changed paths:
M lib/galaxy/util/path/__init__.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
Log Message:
-----------
Merge pull request #2 from natefoo/bwlang-import_dirs_check_whitelist
More general safe_walk function, handles symlinks loops
Commit: 0e0e8e9bd6d461a4e25b49cea2e6753043f747e0
https://github.com/galaxyproject/galaxy/commit/0e0e8e9bd6d461a4e25b49cea2e6…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M lib/galaxy/util/path/__init__.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
Log Message:
-----------
Merge pull request #5596 from bwlang/import_dirs_check_whitelist
allows whitelisted symlinks to be imported from
Compare: https://github.com/galaxyproject/galaxy/compare/a847ce20965e...0e0e8e9bd6d4
1
0
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: a461bf5adf0e0eea3aa50f0c44977101a00f38be
https://github.com/galaxyproject/usegalaxy-playbook/commit/a461bf5adf0e0eea…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M env/main/files/galaxy/config/tool_conf.xml
Log Message:
-----------
unhide cut and cat
1
0
Branch: refs/heads/master
Home: https://github.com/galaxyproject/usegalaxy-playbook
Commit: 9520aeab701220229f7b5c57a45b9364f91883b7
https://github.com/galaxyproject/usegalaxy-playbook/commit/9520aeab70122022…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M env/main/files/galaxy/config/tool_conf.xml
Log Message:
-----------
hide tools from Main
that are no longer wanted
1
0
Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: 7254d55e8b192ff4387ef6a276e202db5821ca60
https://github.com/galaxyproject/galaxy/commit/7254d55e8b192ff4387ef6a276e2…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Remove href from grid sorting links
Commit: 7ffabb1df3f6feb11a3746c2f27bc762b1af29c7
https://github.com/galaxyproject/galaxy/commit/7ffabb1df3f6feb11a3746c2f27b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Remove unused variable
Commit: e01f9fa1b89e6a5fd12f9ef98ddb005959e1b761
https://github.com/galaxyproject/galaxy/commit/e01f9fa1b89e6a5fd12f9ef98ddb…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M client/galaxy/scripts/mvc/grid/grid-template.js
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
Merge pull request #5634 from guerler/fix_async_grid_links
[18.01] Remove href from grid sorting links
Compare: https://github.com/galaxyproject/galaxy/compare/41910f824ea3...e01f9fa1b89e
1
0
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: c47516a1cb3f1e66fb24fcd78e078fd04d77f9a6
https://github.com/galaxyproject/galaxy/commit/c47516a1cb3f1e66fb24fcd78e07…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-08 (Mon, 08 Jan 2018)
Changed paths:
A client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/mvc/history/options-menu.js
A lib/galaxy/util/create_history_template.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/login.bundled.js
M static/scripts/mvc/history/options-menu.js
R templates/webapps/galaxy/history/display_structured.mako
Log Message:
-----------
Remove show history structure mako
Commit: 9c8fb8f9d97ba0d5ab6eaec74ea62706483a9148
https://github.com/galaxyproject/galaxy/commit/9c8fb8f9d97ba0d5ab6eaec74ea6…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-13 (Sat, 13 Jan 2018)
Changed paths:
M client/galaxy/scripts/components/DisplayStructured.vue
M lib/galaxy/util/create_history_template.py
M static/scripts/bundled/analysis.bundled.js
Log Message:
-----------
Update the styling
Commit: c1ec73aa58467d255dd3aa8ca43bb20721b5f4e3
https://github.com/galaxyproject/galaxy/commit/c1ec73aa58467d255dd3aa8ca43b…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-13 (Sat, 13 Jan 2018)
Changed paths:
M client/galaxy/scripts/components/Citations.vue
M client/galaxy/scripts/components/HistoryImport.vue
M client/galaxy/scripts/components/Message.vue
M client/galaxy/scripts/components/admin/BaseGrid.vue
M client/galaxy/scripts/components/admin/DataManagerGrid.vue
M client/galaxy/scripts/components/admin/DataTables.vue
M client/galaxy/scripts/components/admin/DataTablesGrid.vue
M client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/nls/zh/locale.js
M client/package.json
M client/webpack.config.js
M client/yarn.lock
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
M doc/source/admin/production.md
M lib/galaxy/datatypes/msa.py
A lib/galaxy/datatypes/test/infernal_model.cm
M lib/galaxy/model/migrate/check.py
M lib/galaxy/workflow/modules.py
M scripts/common_startup.sh
M scripts/db_shell.py
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/mvc/dataset/dataset-error.js
M static/scripts/nls/zh/locale.js
M test/api/test_workflows.py
Log Message:
-----------
Merging with dev
Commit: e9755e111ac6f3e3d8412d539ecd91fb6a98cc31
https://github.com/galaxyproject/galaxy/commit/e9755e111ac6f3e3d8412d539ecd…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-13 (Sat, 13 Jan 2018)
Changed paths:
M lib/galaxy/util/create_history_template.py
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Remove extra spacings around the braces
Commit: 5d5260260b3f44cbc9aac5018f41166006380c12
https://github.com/galaxyproject/galaxy/commit/5d5260260b3f44cbc9aac5018f41…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-14 (Sun, 14 Jan 2018)
Changed paths:
M client/galaxy/scripts/components/DisplayStructured.vue
Log Message:
-----------
Remove unused variables
Commit: 30a3ebee184de55755141b5baa1f495b2cf2b2ec
https://github.com/galaxyproject/galaxy/commit/30a3ebee184de55755141b5baa1f…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-14 (Sun, 14 Jan 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/components/HistoryView.vue
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/libs.bundled.js
Log Message:
-----------
Update structure to replace history/view mako file
Commit: 394ae3340c52d632d2cc58929448352eae42dbdb
https://github.com/galaxyproject/galaxy/commit/394ae3340c52d632d2cc58929448…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-14 (Sun, 14 Jan 2018)
Changed paths:
M client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/components/HistoryView.vue
M lib/galaxy/util/create_history_template.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/login.bundled.js
Log Message:
-----------
Add view feature for a history in the list of histories
Commit: 92c7900356842fce23504bca607d4712b8adc8c8
https://github.com/galaxyproject/galaxy/commit/92c7900356842fce23504bca607d…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-14 (Sun, 14 Jan 2018)
Changed paths:
R templates/webapps/galaxy/history/view.mako
Log Message:
-----------
Remove history/view.mako file
Commit: 2e8ce77fc099481ec29bc5f65390640260073ec3
https://github.com/galaxyproject/galaxy/commit/2e8ce77fc099481ec29bc5f65390…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/tools/__init__.py
M scripts/common_startup.sh
Log Message:
-----------
Merge branch 'dev' of https://github.com/bgruening/galaxy into history_structure
Commit: 523bccdef829e03cbe84144d7139c5a9b163ba1b
https://github.com/galaxyproject/galaxy/commit/523bccdef829e03cbe84144d7139…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths:
M lib/galaxy/util/create_history_template.py
Log Message:
-----------
Update the dataset url
Commit: f2b0a3936e33081999103023f52397ecef492512
https://github.com/galaxyproject/galaxy/commit/f2b0a3936e33081999103023f523…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths:
M client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/components/HistoryView.vue
M client/galaxy/scripts/mvc/history/options-menu.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/analysis.bundled.js
M static/scripts/mvc/history/options-menu.js
Log Message:
-----------
Update styling
Commit: dab7248c4e2bc6975052136a28f614321574dc78
https://github.com/galaxyproject/galaxy/commit/dab7248c4e2bc6975052136a28f6…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths:
M client/galaxy/scripts/components/DisplayStructured.vue
Log Message:
-----------
Remove console.log statement from vue
Commit: 99f744f8353b37fd4d0a43b2ed9fe1493846c844
https://github.com/galaxyproject/galaxy/commit/99f744f8353b37fd4d0a43b2ed9f…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths:
M client/galaxy/scripts/components/HistoryView.vue
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/extended.bundled.js
M static/scripts/bundled/libs.bundled.js
M static/scripts/mvc/library/library-dataset-view.js
Log Message:
-----------
Update json structure and add static files
Commit: 29695ecf52ba1ce1ea07d2e1158e1f7fe5432678
https://github.com/galaxyproject/galaxy/commit/29695ecf52ba1ce1ea07d2e1158e…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-16 (Tue, 16 Jan 2018)
Changed paths:
M lib/galaxy/util/create_history_template.py
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Fix build fail issues
Commit: e619faefe405fe30c1d2a06b4d337e275f06ee5f
https://github.com/galaxyproject/galaxy/commit/e619faefe405fe30c1d2a06b4d33…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2018-01-17 (Wed, 17 Jan 2018)
Changed paths:
M lib/galaxy/util/create_history_template.py
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Fix scripts
Commit: 3f8b38f4cb90e26cb13533a44c41e3756af68db0
https://github.com/galaxyproject/galaxy/commit/3f8b38f4cb90e26cb13533a44c41…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-28 (Sun, 28 Jan 2018)
Changed paths:
M .ci/jenkins/api/run_tests.sh
M .ci/jenkins/selenium-compose/run_tests.sh
M .ci/jenkins/selenium/run_tests.sh
M .gitignore
M .travis.yml
M Makefile
M client/galaxy/scripts/apps/extended.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/history.less
M config/auth_conf.xml.sample
M config/datatypes_conf.xml.sample
R config/galaxy.ini.sample
A config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
M config/tool_shed.yml.sample
M doc/Makefile
A doc/source/admin/_inc_proxy_prereq.rst
A doc/source/admin/_inc_proxy_serving_root.rst
A doc/source/admin/_inc_proxy_ssl.rst
A doc/source/admin/apache.md
M doc/source/admin/authentication.md
M doc/source/admin/cluster.md
M doc/source/admin/conda_faq.rst
A doc/source/admin/config.rst
A doc/source/admin/config_logging.rst
M doc/source/admin/dependency_resolvers.rst
A doc/source/admin/galaxy_options.rst
M doc/source/admin/index.rst
M doc/source/admin/jobs.md
A doc/source/admin/nginx.md
A doc/source/admin/options.rst
M doc/source/admin/production.md
A doc/source/admin/proxy_package_layout.rst
M doc/source/admin/reports.md
M doc/source/admin/reports.rst
M doc/source/admin/scaling.md
R doc/source/admin/special_topics/apache.md
M doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/chat.rst
M doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
M doc/source/admin/special_topics/interactive_environments.rst
R doc/source/admin/special_topics/nginx.md
M doc/source/admin/special_topics/performance_tracking.rst
M doc/source/admin/special_topics/webhooks.rst
M doc/source/admin/tool_panel.rst
M doc/source/conf.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
A lib/galaxy/auth/util.py
M lib/galaxy/config.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
A lib/galaxy/datatypes/converters/sam_to_bam_native.xml
A lib/galaxy/datatypes/phylip.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/test.phylip
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/develop/Pipfile
M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/dictifiable.py
M lib/galaxy/util/handlers.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/version.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/webapp.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/configuration.py
M lib/galaxy/webapps/galaxy/api/histories.py
M lib/galaxy/webapps/galaxy/api/jobs.py
A lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A lib/galaxy/webapps/galaxy/uwsgi_schema.yml
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/config_schema.yml
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/util/admin_util.py
M run_tests.sh
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
A scripts/common_startup_variables.sh
M scripts/db_shell.py
M scripts/functional_tests.py
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
A scripts/maintenance.sh
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
M templates/user/register.mako
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
A test-data/bam_native_from_sam.bam
M test-data/sam_with_header.sam
M test/base/driver_util.py
M test/base/integration_util.py
M test/docker/base/run_test_wrapper.sh
A test/functional/tools/job_environment_default.xml
A test/functional/tools/job_environment_default_legacy.xml
A test/functional/tools/job_environment_explicit_shared_home.xml
A test/functional/tools/mulled_example_explicit.xml
A test/functional/tools/mulled_example_simple.xml
A test/functional/tools/multi_output_recurse.xml
A test/functional/tools/sam_to_bam_native.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/integration/dockerized_job_conf.xml
A test/integration/sets_tmp_dir_expression_job_conf.xml
A test/integration/sets_tmp_dir_to_true_job_conf.xml
A test/integration/simple_job_conf.xml
A test/integration/test_dockerized_jobs.py
A test/integration/test_job_environments.py
M test/manual/launch_and_run.sh
A test/unit/config/1705_allow_path_paste/config/galaxy.ini
A test/unit/config/__init__.py
M test/unit/config/test_config_manage.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_evaluation.py
M tools/data_source/microbial_import_code.py
Log Message:
-----------
Merging with dev
Commit: dc3fcadda12a71c0eb8e508b88538ca09741d529
https://github.com/galaxyproject/galaxy/commit/dc3fcadda12a71c0eb8e508b8853…
Author: anup kumar <anup.rulez(a)gmail.com>
Date: 2018-01-28 (Sun, 28 Jan 2018)
Changed paths:
M lib/galaxy/util/create_history_template.py
M lib/galaxy/webapps/galaxy/controllers/history.py
Log Message:
-----------
Merge branch 'history_structure' of https://github.com/bgruening/galaxy into history_structure
Commit: da23ed2ec60a851b011902acd6498ccddcb03f64
https://github.com/galaxyproject/galaxy/commit/da23ed2ec60a851b011902acd649…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2018-02-06 (Tue, 06 Feb 2018)
Changed paths:
M .ci/check_py3_compatibility.sh
M .ci/flake8_blacklist.txt
M .ci/flake8_wrapper.sh
M .ci/flake8_wrapper_docstrings.sh
M .ci/jenkins/api/run_tests.sh
M .ci/jenkins/selenium-compose/run_tests.sh
M .ci/jenkins/selenium/run_tests.sh
M .gitignore
M .travis.yml
M Makefile
M client/galaxy/scripts/apps/extended.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.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/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/mvc/tool/tool-form-composite.js
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/qunit/test-app.js
M client/galaxy/scripts/qunit/tests/page_tests.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/dataset.less
M client/galaxy/style/less/history.less
M client/galaxy/style/less/ui/icon-btn.less
M config/auth_conf.xml.sample
M config/datatypes_conf.xml.sample
R config/galaxy.ini.sample
A config/galaxy.yml.sample
M config/job_conf.xml.sample_advanced
A config/plugins/webhooks/demo/search/config.yml
R config/plugins/webhooks/demo/search/config/searchover.yaml
A config/plugins/webhooks/demo/search/script.js
R config/plugins/webhooks/demo/search/static/script.js
R config/plugins/webhooks/demo/search/static/styles.css
A config/plugins/webhooks/demo/search/styles.css
A config/plugins/webhooks/demo/tool_list/__init__.py
A config/plugins/webhooks/demo/tool_list/config.yml
R config/plugins/webhooks/demo/tool_list/config/tool_list.yml
R config/plugins/webhooks/demo/tool_list/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/__init__.py
A config/plugins/webhooks/demo/tour_generator/config.yml
R config/plugins/webhooks/demo/tour_generator/config/tour_generator.yml
R config/plugins/webhooks/demo/tour_generator/helper/__init__.py
A config/plugins/webhooks/demo/tour_generator/script.js
R config/plugins/webhooks/demo/tour_generator/static/script.js
R config/plugins/webhooks/demo/tour_generator/static/styles.css
A config/plugins/webhooks/demo/tour_generator/styles.css
M config/tool_shed.yml.sample
M doc/Makefile
A doc/source/admin/_inc_proxy_prereq.rst
A doc/source/admin/_inc_proxy_serving_root.rst
A doc/source/admin/_inc_proxy_ssl.rst
A doc/source/admin/apache.md
M doc/source/admin/authentication.md
M doc/source/admin/cluster.md
M doc/source/admin/conda_faq.rst
A doc/source/admin/config.rst
A doc/source/admin/config_logging.rst
M doc/source/admin/dependency_resolvers.rst
M doc/source/admin/framework_dependencies.rst
A doc/source/admin/galaxy_options.rst
M doc/source/admin/index.rst
M doc/source/admin/jobs.md
A doc/source/admin/nginx.md
A doc/source/admin/options.rst
M doc/source/admin/production.md
A doc/source/admin/proxy_package_layout.rst
M doc/source/admin/reports.md
M doc/source/admin/reports.rst
M doc/source/admin/scaling.md
R doc/source/admin/special_topics/apache.md
M doc/source/admin/special_topics/bug_reports.rst
M doc/source/admin/special_topics/chat.rst
M doc/source/admin/special_topics/ftp.md
M doc/source/admin/special_topics/index.rst
M doc/source/admin/special_topics/interactive_environments.rst
R doc/source/admin/special_topics/nginx.md
M doc/source/admin/special_topics/performance_tracking.rst
M doc/source/admin/special_topics/webhooks.rst
M doc/source/admin/tool_panel.rst
M doc/source/conf.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
A lib/galaxy/auth/util.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/datatypes/binary.py
A lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml
M lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam.py
A lib/galaxy/datatypes/converters/sam_to_bam_native.xml
A lib/galaxy/datatypes/phylip.py
M lib/galaxy/datatypes/sniff.py
A lib/galaxy/datatypes/test/test.phylip
R lib/galaxy/dependencies/conda-environment.txt
A lib/galaxy/dependencies/conda-file.sh
M lib/galaxy/dependencies/conditional-requirements.txt
M lib/galaxy/dependencies/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/develop/Pipfile
M lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/data_manager/manager.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/commands.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/docker_util.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/merge_collection.xml
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parser/interface.py
M lib/galaxy/tools/parser/output_collection_def.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/integrated_panel.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/util/dictifiable.py
M lib/galaxy/util/facts.py
M lib/galaxy/util/handlers.py
M lib/galaxy/util/logging/__init__.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/helpers/__init__.py
A lib/galaxy/web/framework/helpers/tags.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/message.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/configuration.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/webhooks.py
M lib/galaxy/webapps/galaxy/buildapp.py
A lib/galaxy/webapps/galaxy/config_schema.yml
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A lib/galaxy/webapps/galaxy/uwsgi_schema.yml
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/config_schema.yml
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webhooks/__init__.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/galaxy_install/migrate/common.py
M lib/tool_shed/util/admin_util.py
M lib/tool_shed/util/repository_util.py
M lib/tool_shed/util/xml_util.py
M run_tests.sh
M scripts/cleanup_datasets/cleanup_datasets.py
M scripts/common_startup.sh
M scripts/common_startup_functions.sh
A scripts/common_startup_variables.sh
M scripts/db_shell.py
A scripts/dump_library_paths.py
M scripts/functional_tests.py
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
A scripts/maintenance.sh
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_tool_shed.sh
M scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py
R static/scripts/admin.toolshed.js
R static/scripts/bundled/admin.bundled.js
R static/scripts/bundled/analysis.bundled.js
R static/scripts/bundled/extended.bundled.js
R static/scripts/bundled/libs.bundled.js
R static/scripts/bundled/login.bundled.js
R static/scripts/galaxy.interactive_environments.js
R static/scripts/galaxy.js
R static/scripts/galaxy.library.js
R static/scripts/galaxy.pages.js
R static/scripts/i18n.js
R static/scripts/layout/generic-nav-view.js
R static/scripts/layout/masthead.js
R static/scripts/layout/menu.js
R static/scripts/layout/modal.js
R static/scripts/layout/page.js
R static/scripts/layout/panel.js
R static/scripts/layout/router.js
R static/scripts/layout/scratchbook.js
R static/scripts/legacy/grid/grid-model.js
R static/scripts/legacy/grid/grid-template.js
R static/scripts/legacy/grid/grid-view.js
R static/scripts/libs/backbone.js
R static/scripts/libs/bbi/bigwig.js
R static/scripts/libs/bbi/jquery-ajax-native.js
R static/scripts/libs/bbi/jszlib.js
R static/scripts/libs/bbi/spans.js
R static/scripts/libs/bibtexParse.js
R static/scripts/libs/bootstrap-tour.js
R static/scripts/libs/bootstrap.js
R static/scripts/libs/d3.js
R static/scripts/libs/farbtastic.js
R static/scripts/libs/jquery.sparklines.js
R static/scripts/libs/jquery/jquery-ui.js
R static/scripts/libs/jquery/jquery.autocomplete.js
R static/scripts/libs/jquery/jquery.complexify.js
R static/scripts/libs/jquery/jquery.cookie.js
R static/scripts/libs/jquery/jquery.dynatree.js
R static/scripts/libs/jquery/jquery.event.drag.js
R static/scripts/libs/jquery/jquery.event.drop.js
R static/scripts/libs/jquery/jquery.event.hover.js
R static/scripts/libs/jquery/jquery.form.js
R static/scripts/libs/jquery/jquery.js
R static/scripts/libs/jquery/jquery.migrate.js
R static/scripts/libs/jquery/jquery.mousewheel.js
R static/scripts/libs/jquery/jquery.rating.js
R static/scripts/libs/jquery/jquery.wymeditor.js
R static/scripts/libs/jquery/jstorage.js
R static/scripts/libs/jquery/jstree.js
R static/scripts/libs/jquery/select2.js
R static/scripts/libs/raven.js
R static/scripts/libs/require.js
R static/scripts/libs/toastr.js
R static/scripts/libs/underscore.js
R static/scripts/mvc/annotation.js
R static/scripts/mvc/base-mvc.js
R static/scripts/mvc/base/controlled-fetch-collection.js
R static/scripts/mvc/collection/base-creator.js
R static/scripts/mvc/collection/collection-li-edit.js
R static/scripts/mvc/collection/collection-li.js
R static/scripts/mvc/collection/collection-model.js
R static/scripts/mvc/collection/collection-view-edit.js
R static/scripts/mvc/collection/collection-view.js
R static/scripts/mvc/collection/list-collection-creator.js
R static/scripts/mvc/collection/list-of-pairs-collection-creator.js
R static/scripts/mvc/collection/pair-collection-creator.js
R static/scripts/mvc/dataset/data.js
R static/scripts/mvc/dataset/dataset-choice.js
R static/scripts/mvc/dataset/dataset-edit-attributes.js
R static/scripts/mvc/dataset/dataset-error.js
R static/scripts/mvc/dataset/dataset-li-edit.js
R static/scripts/mvc/dataset/dataset-li.js
R static/scripts/mvc/dataset/dataset-list.js
R static/scripts/mvc/dataset/dataset-model.js
R static/scripts/mvc/dataset/states.js
R static/scripts/mvc/form/form-data.js
R static/scripts/mvc/form/form-input.js
R static/scripts/mvc/form/form-parameters.js
R static/scripts/mvc/form/form-repeat.js
R static/scripts/mvc/form/form-section.js
R static/scripts/mvc/form/form-view.js
R static/scripts/mvc/form/form-wrapper.js
R static/scripts/mvc/grid/grid-model.js
R static/scripts/mvc/grid/grid-shared.js
R static/scripts/mvc/grid/grid-template.js
R static/scripts/mvc/grid/grid-view.js
R static/scripts/mvc/history/copy-dialog.js
R static/scripts/mvc/history/hda-li-edit.js
R static/scripts/mvc/history/hda-li.js
R static/scripts/mvc/history/hda-model.js
R static/scripts/mvc/history/hdca-li-edit.js
R static/scripts/mvc/history/hdca-li.js
R static/scripts/mvc/history/hdca-model.js
R static/scripts/mvc/history/history-content-model.js
R static/scripts/mvc/history/history-contents.js
R static/scripts/mvc/history/history-item-li.js
R static/scripts/mvc/history/history-list.js
R static/scripts/mvc/history/history-model.js
R static/scripts/mvc/history/history-preferences.js
R static/scripts/mvc/history/history-structure-view.js
R static/scripts/mvc/history/history-view-annotated.js
R static/scripts/mvc/history/history-view-edit-current.js
R static/scripts/mvc/history/history-view-edit.js
R static/scripts/mvc/history/history-view.js
R static/scripts/mvc/history/job-dag.js
R static/scripts/mvc/history/job-states-model.js
R static/scripts/mvc/history/multi-panel.js
R static/scripts/mvc/history/options-menu.js
R static/scripts/mvc/job/job-li.js
R static/scripts/mvc/job/job-model.js
R static/scripts/mvc/job/job-params.js
R static/scripts/mvc/lazy/lazy-limited.js
R static/scripts/mvc/library/library-dataset-view.js
R static/scripts/mvc/library/library-folder-view.js
R static/scripts/mvc/library/library-folderlist-view.js
R static/scripts/mvc/library/library-folderrow-view.js
R static/scripts/mvc/library/library-foldertoolbar-view.js
R static/scripts/mvc/library/library-library-view.js
R static/scripts/mvc/library/library-librarylist-view.js
R static/scripts/mvc/library/library-libraryrow-view.js
R static/scripts/mvc/library/library-librarytoolbar-view.js
R static/scripts/mvc/library/library-model.js
R static/scripts/mvc/library/library-util.js
R static/scripts/mvc/list/list-item.js
R static/scripts/mvc/list/list-view.js
R static/scripts/mvc/tag.js
R static/scripts/mvc/tool/tool-form-base.js
R static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form.js
R static/scripts/mvc/tool/tool-genomespace.js
R static/scripts/mvc/tool/tools.js
R static/scripts/mvc/toolshed/categories-view.js
R static/scripts/mvc/toolshed/repo-queue-view.js
R static/scripts/mvc/toolshed/repo-status-view.js
R static/scripts/mvc/toolshed/repositories-view.js
R static/scripts/mvc/toolshed/repository-queue-view.js
R static/scripts/mvc/toolshed/repository-view.js
R static/scripts/mvc/toolshed/shed-list-view.js
R static/scripts/mvc/toolshed/toolshed-model.js
R static/scripts/mvc/toolshed/util.js
R static/scripts/mvc/toolshed/workflows-view.js
R static/scripts/mvc/tours.js
R static/scripts/mvc/ui/error-modal.js
R static/scripts/mvc/ui/icon-button.js
R static/scripts/mvc/ui/popup-menu.js
R static/scripts/mvc/ui/ui-buttons.js
R static/scripts/mvc/ui/ui-color-picker.js
R static/scripts/mvc/ui/ui-drilldown.js
R static/scripts/mvc/ui/ui-frames.js
R static/scripts/mvc/ui/ui-list.js
R static/scripts/mvc/ui/ui-misc.js
R static/scripts/mvc/ui/ui-modal.js
R static/scripts/mvc/ui/ui-options.js
R static/scripts/mvc/ui/ui-popover.js
R static/scripts/mvc/ui/ui-portlet.js
R static/scripts/mvc/ui/ui-select-content.js
R static/scripts/mvc/ui/ui-select-default.js
R static/scripts/mvc/ui/ui-select-ftp.js
R static/scripts/mvc/ui/ui-select-genomespace.js
R static/scripts/mvc/ui/ui-select-library.js
R static/scripts/mvc/ui/ui-select.js
R static/scripts/mvc/ui/ui-slider.js
R static/scripts/mvc/ui/ui-table.js
R static/scripts/mvc/ui/ui-tabs.js
R static/scripts/mvc/ui/ui-thumbnails.js
R static/scripts/mvc/upload/collection/collection-row.js
R static/scripts/mvc/upload/collection/collection-view.js
R static/scripts/mvc/upload/composite/composite-row.js
R static/scripts/mvc/upload/composite/composite-view.js
R static/scripts/mvc/upload/default/default-row.js
R static/scripts/mvc/upload/default/default-view.js
R static/scripts/mvc/upload/upload-button.js
R static/scripts/mvc/upload/upload-extension.js
R static/scripts/mvc/upload/upload-ftp.js
R static/scripts/mvc/upload/upload-model.js
R static/scripts/mvc/upload/upload-settings.js
R static/scripts/mvc/upload/upload-view.js
R static/scripts/mvc/user/user-custom-builds.js
R static/scripts/mvc/user/user-model.js
R static/scripts/mvc/user/user-preferences.js
R static/scripts/mvc/user/user-quotameter.js
R static/scripts/mvc/visualization/visualization-model.js
R static/scripts/mvc/webhooks.js
R static/scripts/mvc/workflow/workflow-canvas.js
R static/scripts/mvc/workflow/workflow-connector.js
R static/scripts/mvc/workflow/workflow-forms.js
R static/scripts/mvc/workflow/workflow-icons.js
R static/scripts/mvc/workflow/workflow-manager.js
R static/scripts/mvc/workflow/workflow-model.js
R static/scripts/mvc/workflow/workflow-node.js
R static/scripts/mvc/workflow/workflow-terminals.js
R static/scripts/mvc/workflow/workflow-view-data.js
R static/scripts/mvc/workflow/workflow-view-node.js
R static/scripts/mvc/workflow/workflow-view-terminals.js
R static/scripts/mvc/workflow/workflow-view.js
R static/scripts/mvc/workflow/workflow.js
R static/scripts/nls/de/locale.js
R static/scripts/nls/es/locale.js
R static/scripts/nls/fr/locale.js
R static/scripts/nls/ja/locale.js
R static/scripts/nls/locale.js
R static/scripts/nls/zh/locale.js
R static/scripts/onload.js
R static/scripts/polyfills.js
R static/scripts/reports/run_stats.js
R static/scripts/toolshed/groups/group-detail-view.js
R static/scripts/toolshed/groups/group-list-view.js
R static/scripts/toolshed/groups/group-listrow-view.js
R static/scripts/toolshed/groups/group-model.js
R static/scripts/toolshed/toolshed.groups.js
R static/scripts/ui/autocom_tagging.js
R static/scripts/ui/editable-text.js
R static/scripts/ui/fa-icon-button.js
R static/scripts/ui/filter-control.js
R static/scripts/ui/hoverhighlight.js
R static/scripts/ui/loading-indicator.js
R static/scripts/ui/mode-button.js
R static/scripts/ui/pagination.js
R static/scripts/ui/peek-column-selector.js
R static/scripts/ui/popupmenu.js
R static/scripts/ui/scroll-panel.js
R static/scripts/ui/search-input.js
R static/scripts/utils/add-logging.js
R static/scripts/utils/ajax-queue.js
R static/scripts/utils/async-save-text.js
R static/scripts/utils/config.js
R static/scripts/utils/deferred.js
R static/scripts/utils/graph.js
R static/scripts/utils/levenshtein.js
R static/scripts/utils/localization.js
R static/scripts/utils/metrics-logger.js
R static/scripts/utils/natural-sort.js
R static/scripts/utils/query-string-parsing.js
R static/scripts/utils/uploadbox.js
R static/scripts/utils/utils.js
R static/scripts/viz/bbi-data-manager.js
R static/scripts/viz/circster.js
R static/scripts/viz/phyloviz.js
R static/scripts/viz/sweepster.js
R static/scripts/viz/trackster.js
R static/scripts/viz/trackster/filters.js
R static/scripts/viz/trackster/painters.js
R static/scripts/viz/trackster/slotting.js
R static/scripts/viz/trackster/tracks.js
R static/scripts/viz/trackster/util.js
R static/scripts/viz/visualization.js
R static/scripts/viz/viz_views.js
M templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako
M templates/admin/tool_shed_repository/manage_repository_tool_dependencies.mako
M templates/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako
M templates/galaxy_client_app.mako
M templates/user/register.mako
M templates/webapps/galaxy/dataset/security_common.mako
M templates/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako
M templates/webapps/tool_shed/repository/tool_form.mako
A test-data/bam_native_from_sam.bam
M test-data/sam_with_header.sam
M test/api/test_tools.py
M test/api/test_webhooks.py
M test/api/test_workflows.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/workflows_format_2/converter.py
M test/docker/base/run_test_wrapper.sh
M test/functional/tools/collection_creates_dynamic_list_of_pairs.xml
A test/functional/tools/job_environment_default.xml
A test/functional/tools/job_environment_default_legacy.xml
A test/functional/tools/job_environment_explicit_shared_home.xml
A test/functional/tools/mulled_example_explicit.xml
A test/functional/tools/mulled_example_simple.xml
A test/functional/tools/multi_output_recurse.xml
A test/functional/tools/sam_to_bam_native.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/twilltestcase.py
A test/functional/webhooks/history_test1/config.yml
R test/functional/webhooks/history_test1/config/history_test1.yml
A test/functional/webhooks/history_test2/config.yml
R test/functional/webhooks/history_test2/config/history_test2.yml
A test/functional/webhooks/masthead_test/config.yml
R test/functional/webhooks/masthead_test/config/masthead_test.yml
A test/functional/webhooks/phdcomics/__init__.py
A test/functional/webhooks/phdcomics/config.yaml
R test/functional/webhooks/phdcomics/config/phdcomics.yaml
R test/functional/webhooks/phdcomics/helper/__init__.py
A test/functional/webhooks/phdcomics/script.js
R test/functional/webhooks/phdcomics/static/script.js
R test/functional/webhooks/phdcomics/static/styles.css
A test/functional/webhooks/phdcomics/styles.css
A test/functional/webhooks/trans_object/__init__.py
A test/functional/webhooks/trans_object/config.yaml
R test/functional/webhooks/trans_object/config/trans_object.yaml
R test/functional/webhooks/trans_object/helper/__init__.py
A test/functional/webhooks/xkcd/config.yml
R test/functional/webhooks/xkcd/config/xkcd.yml
A test/functional/webhooks/xkcd/script.js
R test/functional/webhooks/xkcd/static/script.js
R test/functional/webhooks/xkcd/static/styles.css
A test/functional/webhooks/xkcd/styles.css
A test/integration/dockerized_job_conf.xml
A test/integration/sets_tmp_dir_expression_job_conf.xml
A test/integration/sets_tmp_dir_to_true_job_conf.xml
A test/integration/simple_job_conf.xml
A test/integration/test_dockerized_jobs.py
A test/integration/test_job_environments.py
M test/manual/launch_and_run.sh
M test/selenium_tests/test_tool_describing_tours.py
M test/shed_functional/base/twilltestcase.py
A test/unit/config/1705_allow_path_paste/config/galaxy.ini
A test/unit/config/__init__.py
M test/unit/config/test_config_manage.py
M test/unit/jobs/test_mapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/test_HistoryManager.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_evaluation.py
M tools/data_source/microbial_import_code.py
M tox.ini
Log Message:
-----------
Merge with dev
Commit: 8772dbbb38664edfb6b6d472553ad7e421b35b0b
https://github.com/galaxyproject/galaxy/commit/8772dbbb38664edfb6b6d472553a…
Author: anuprulez <anup.rulez(a)gmail.com>
Date: 2018-02-06 (Tue, 06 Feb 2018)
Log Message:
-----------
Merge branch 'history_structure' of https://github.com/bgruening/galaxy into history_structure
Commit: 73db0a5e80fa6cc528ec9170bd443971c001b32c
https://github.com/galaxyproject/galaxy/commit/73db0a5e80fa6cc528ec9170bd44…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/mvc/history/options-menu.js
M lib/galaxy/webapps/galaxy/buildapp.py
M static/style/blue/base.css
Log Message:
-----------
Move show_structure to first class client route enabling direct nav, linking, etc. Minor cleanup
Commit: 3c0344bf15fe40f662586ac212e34bf5963c3345
https://github.com/galaxyproject/galaxy/commit/3c0344bf15fe40f662586ac212e3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths:
M client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/components/HistoryView.vue
Log Message:
-----------
Vue formatting via prettier.
Commit: baeb99e54720767066e8a1e96c9f237c2fcce890
https://github.com/galaxyproject/galaxy/commit/baeb99e54720767066e8a1e96c9f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths:
M client/galaxy/scripts/components/DisplayStructured.vue
Log Message:
-----------
Use explicit imports instead of relying on bundleEntries. Kill toastr for axios error -- unnecessary.
Commit: 3c25883d5522c9763a16b977343a50a84cc28ddc
https://github.com/galaxyproject/galaxy/commit/3c25883d5522c9763a16b977343a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths:
M client/galaxy/scripts/components/HistoryView.vue
Log Message:
-----------
Remove another toastr error -- this sort of thing should be console; reporting http errors in the main UI isn't great UX
Commit: 433472a315ced57e033583ef0569d95e36d13bc3
https://github.com/galaxyproject/galaxy/commit/433472a315ced57e033583ef0569…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths:
M client/galaxy/scripts/apps/extended.js
M client/galaxy/scripts/components/HistoryView.vue
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
Log Message:
-----------
refactor history view entrypoint out of extended bundle into history-view; swap HistoryView.vue to use new points. Minor import refactoring/cleanup, too.
Commit: ee3b25c68f7ceb7fb3022d4002362806eabb38c0
https://github.com/galaxyproject/galaxy/commit/ee3b25c68f7ceb7fb3022d400236…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths:
M client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/components/HistoryView.vue
Log Message:
-----------
V-cloak hides uncompiled templates -- we precompile everything (and intend to, always) so this isn't necessary
Commit: 97fac3983d894df0b6c75a9c2f0ea3b54421a774
https://github.com/galaxyproject/galaxy/commit/97fac3983d894df0b6c75a9c2f0e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths:
M client/galaxy/scripts/components/DisplayStructured.vue
M client/galaxy/scripts/components/HistoryView.vue
Log Message:
-----------
Slightly better temporary error handling for new vue components.
Commit: 6b72952e953c118234357585cb6d3a50c3df4837
https://github.com/galaxyproject/galaxy/commit/6b72952e953c118234357585cb6d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-19 (Mon, 19 Feb 2018)
Changed paths:
M Makefile
M client/galaxy/scripts/apps/analysis.js
A client/galaxy/scripts/apps/chart.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/scratchbook.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/tool/tool-genomespace.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
A client/galaxy/scripts/mvc/visualization/chart/chart-client.js
A client/galaxy/scripts/mvc/visualization/chart/components/model.js
A client/galaxy/scripts/mvc/visualization/chart/components/screenshot.js
A client/galaxy/scripts/mvc/visualization/chart/utilities/datasets.js
A client/galaxy/scripts/mvc/visualization/chart/utilities/jobs.js
A client/galaxy/scripts/mvc/visualization/chart/utilities/series.js
A client/galaxy/scripts/mvc/visualization/chart/views/description.js
A client/galaxy/scripts/mvc/visualization/chart/views/editor.js
A client/galaxy/scripts/mvc/visualization/chart/views/groups.js
A client/galaxy/scripts/mvc/visualization/chart/views/menu.js
A client/galaxy/scripts/mvc/visualization/chart/views/settings.js
A client/galaxy/scripts/mvc/visualization/chart/views/viewer.js
A client/galaxy/scripts/mvc/visualization/visualization-view.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/qunit/tests/ui_tests.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/style/less/base.less
A client/galaxy/style/less/charts.less
M client/galaxy/style/less/galaxy_variables.less
M client/galaxy/style/less/ui.less
M client/package.json
M client/webpack.config.js
M config/datatypes_conf.xml.sample
M config/galaxy.yml.sample
R config/plugins/visualizations/charts/config/charts.xml
R config/plugins/visualizations/charts/package.json
R config/plugins/visualizations/charts/static/client/app.css
R config/plugins/visualizations/charts/static/client/app.js
R config/plugins/visualizations/charts/static/client/components/model.js
R config/plugins/visualizations/charts/static/client/components/screenshot.js
R config/plugins/visualizations/charts/static/client/views/description.js
R config/plugins/visualizations/charts/static/client/views/editor.js
R config/plugins/visualizations/charts/static/client/views/groups.js
R config/plugins/visualizations/charts/static/client/views/settings.js
R config/plugins/visualizations/charts/static/client/views/viewer.js
R config/plugins/visualizations/charts/static/client/views/viewport.js
R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js
R config/plugins/visualizations/charts/static/repository/build/benfred_venn.js.map
R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js
R config/plugins/visualizations/charts/static/repository/build/biojs_drawrnajs.js.map
R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js
R config/plugins/visualizations/charts/static/repository/build/biojs_msa.js.map
R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js
R config/plugins/visualizations/charts/static/repository/build/biojs_phylocanvas.js.map
R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js
R config/plugins/visualizations/charts/static/repository/build/cytoscape_viewer.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_bar.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_boxplot.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_histogram_discrete.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_line.js.map
R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js
R config/plugins/visualizations/charts/static/repository/build/jqplot_scatter.js.map
R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js
R config/plugins/visualizations/charts/static/repository/build/ngl_viewer.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_horizontal_stacked.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_bar_stacked.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_histogram_discrete.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_line.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_line_focus.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_pie.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_scatter.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_full.js.map
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js
R config/plugins/visualizations/charts/static/repository/build/nvd3_stackedarea_stream.js.map
R config/plugins/visualizations/charts/static/repository/build/others_example.js
R config/plugins/visualizations/charts/static/repository/build/others_example.js.map
R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js
R config/plugins/visualizations/charts/static/repository/build/others_heatmap.js.map
R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js
R config/plugins/visualizations/charts/static/repository/build/others_heatmap_cluster.js.map
R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js
R config/plugins/visualizations/charts/static/repository/build/pv_viewer.js.map
R config/plugins/visualizations/charts/static/repository/build/registry.js
R config/plugins/visualizations/charts/static/repository/build/registry.js.map
R config/plugins/visualizations/charts/static/repository/build/registry.tmp.js
R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.css
R config/plugins/visualizations/charts/static/repository/plugins/benfred/venn.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/biojs.msa.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/drawrna.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/layout.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/base.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/connection.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/getnaview.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/loop.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/naview.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/radloop.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/naview/region.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/layouts/radiate/getradiate.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/link.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/linkcol.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/ncanno.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residue.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/residuecol.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/models/structure.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/.Rhistory
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/lasso.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/parsedbr.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/spectrum.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/utils/style.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/annoview.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/optspanel.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/seqpanel.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/drawrnajs/views/vispanel.js
R config/plugins/visualizations/charts/static/repository/plugins/biojs/phylocanvas/phylocanvas.js
R config/plugins/visualizations/charts/static/repository/plugins/cytoscape/cytoscape.js
R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.css
R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.js
R config/plugins/visualizations/charts/static/repository/plugins/jqplot/jquery.jqplot.plugins.js
R config/plugins/visualizations/charts/static/repository/plugins/ngl/viewer.js
R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.css
R config/plugins/visualizations/charts/static/repository/plugins/nvd3/nv.d3.js
R config/plugins/visualizations/charts/static/repository/plugins/pv/viewer.js
R config/plugins/visualizations/charts/static/repository/registry.json
R config/plugins/visualizations/charts/static/repository/utilities/jobs.js
R config/plugins/visualizations/charts/static/repository/utilities/sifjson.js
R config/plugins/visualizations/charts/static/repository/utilities/utils.js
R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/benfred/venn/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/drawrnajs/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/msa/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/biojs/phylocanvas/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/cytoscape/viewer/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/bar/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/boxplot/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/plot-config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/common/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/line/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/jqplot/scatter/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/ngl/viewer/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_horizontal_stacked/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/bar_stacked/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/common/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/histogram_discrete/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/line_focus/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/pie/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/scatter/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_full/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/nvd3/stackedarea_stream/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/example/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/example/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/others/example/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-parameters.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/heatmap-plugin.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/others/heatmap_cluster/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/config.js
R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/logo.png
R config/plugins/visualizations/charts/static/repository/visualizations/pv/viewer/wrapper.js
R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-datasets.js
R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-form.js
R config/plugins/visualizations/charts/static/repository/visualizations/utilities/tabular-utilities.js
R config/plugins/visualizations/charts/templates/charts.mako
R config/plugins/visualizations/charts/webpack.config.js
A config/plugins/visualizations/common/templates/chart_entry_point.mako
M config/plugins/visualizations/common/templates/script_entry_point.mako
A config/plugins/visualizations/cytoscape/config/cytoscape.xml
A config/plugins/visualizations/cytoscape/package.json
A config/plugins/visualizations/cytoscape/src/script.js
A config/plugins/visualizations/cytoscape/static/logo.png
A config/plugins/visualizations/cytoscape/static/script.js
A config/plugins/visualizations/drawrna/config/drawrna.xml
A config/plugins/visualizations/drawrna/package.json
A config/plugins/visualizations/drawrna/src/drawrnajs/drawrna.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/layout.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/base.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/connection.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/getnaview.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/loop.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/naview.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/radloop.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/naview/region.js
A config/plugins/visualizations/drawrna/src/drawrnajs/layouts/radiate/getradiate.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/link.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/linkcol.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/ncanno.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/residue.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/residuecol.js
A config/plugins/visualizations/drawrna/src/drawrnajs/models/structure.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/.Rhistory
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/lasso.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/parsedbr.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/spectrum.js
A config/plugins/visualizations/drawrna/src/drawrnajs/utils/style.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/annoview.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/optspanel.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/seqpanel.js
A config/plugins/visualizations/drawrna/src/drawrnajs/views/vispanel.js
A config/plugins/visualizations/drawrna/src/script.js
A config/plugins/visualizations/drawrna/static/logo.png
A config/plugins/visualizations/drawrna/static/script.js
A config/plugins/visualizations/example/config/example.xml
A config/plugins/visualizations/example/package.json
A config/plugins/visualizations/example/src/script.js
A config/plugins/visualizations/example/static/logo.png
A config/plugins/visualizations/example/static/script.js
R config/plugins/visualizations/graphviz/static/js/jquery.qtip.js
R config/plugins/visualizations/graphviz/static/js/tip_centerwindow.js
R config/plugins/visualizations/graphviz/static/js/tip_followscroll.js
M config/plugins/visualizations/graphviz/templates/graphviz.mako
A config/plugins/visualizations/heatmap/heatmap_cluster/config/heatmap_cluster.xml
A config/plugins/visualizations/heatmap/heatmap_cluster/static/logo.png
A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_default.xml
A config/plugins/visualizations/heatmap/heatmap_default/config/heatmap_shared.xml
A config/plugins/visualizations/heatmap/heatmap_default/package.json
A config/plugins/visualizations/heatmap/heatmap_default/src/colorsets.js
A config/plugins/visualizations/heatmap/heatmap_default/src/script.js
A config/plugins/visualizations/heatmap/heatmap_default/static/logo.png
A config/plugins/visualizations/heatmap/heatmap_default/static/script.js
A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_bar.xml
A config/plugins/visualizations/jqplot/jqplot_bar/config/jqplot_shared.xml
A config/plugins/visualizations/jqplot/jqplot_bar/package.json
A config/plugins/visualizations/jqplot/jqplot_bar/src/script.js
A config/plugins/visualizations/jqplot/jqplot_bar/static/logo.png
A config/plugins/visualizations/jqplot/jqplot_bar/static/script.css
A config/plugins/visualizations/jqplot/jqplot_bar/static/script.js
A config/plugins/visualizations/jqplot/jqplot_box/config/jqplot_box.xml
A config/plugins/visualizations/jqplot/jqplot_box/static/logo.png
A config/plugins/visualizations/jqplot/jqplot_histogram/config/jqplot_histogram.xml
A config/plugins/visualizations/jqplot/jqplot_histogram/static/logo.png
A config/plugins/visualizations/jqplot/jqplot_line/config/jqplot_line.xml
A config/plugins/visualizations/jqplot/jqplot_line/static/logo.png
A config/plugins/visualizations/jqplot/jqplot_scatter/config/jqplot_scatter.xml
A config/plugins/visualizations/jqplot/jqplot_scatter/static/logo.png
A config/plugins/visualizations/msa/config/msa.xml
A config/plugins/visualizations/msa/package.json
A config/plugins/visualizations/msa/src/msa.js
A config/plugins/visualizations/msa/static/logo.png
A config/plugins/visualizations/msa/static/script.js
A config/plugins/visualizations/ngl/config/ngl.xml
A config/plugins/visualizations/ngl/package.json
A config/plugins/visualizations/ngl/src/ngl.js
A config/plugins/visualizations/ngl/src/viewer.js
A config/plugins/visualizations/ngl/static/logo.png
A config/plugins/visualizations/ngl/static/ngl.js
A config/plugins/visualizations/nvd3/nvd3_bar/.babelrc
A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_bar.xml
A config/plugins/visualizations/nvd3/nvd3_bar/config/nvd3_shared.xml
A config/plugins/visualizations/nvd3/nvd3_bar/package.json
A config/plugins/visualizations/nvd3/nvd3_bar/src/nvd3.js
A config/plugins/visualizations/nvd3/nvd3_bar/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.css
A config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js
A config/plugins/visualizations/nvd3/nvd3_bar_stacked/config/nvd3_bar_stacked.xml
A config/plugins/visualizations/nvd3/nvd3_bar_stacked/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_histogram/config/nvd3_histogram.xml
A config/plugins/visualizations/nvd3/nvd3_histogram/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/config/nvd3_histogram_discrete.xml
A config/plugins/visualizations/nvd3/nvd3_histogram_discrete/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_horizontal/config/nvd3_horizontal.xml
A config/plugins/visualizations/nvd3/nvd3_horizontal/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/config/nvd3_horizontal_stacked.xml
A config/plugins/visualizations/nvd3/nvd3_horizontal_stacked/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_line/config/nvd3_line.xml
A config/plugins/visualizations/nvd3/nvd3_line/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_line_focus/config/nvd3_line_focus.xml
A config/plugins/visualizations/nvd3/nvd3_line_focus/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_pie/config/nvd3_pie.xml
A config/plugins/visualizations/nvd3/nvd3_pie/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_scatter/config/nvd3_scatter.xml
A config/plugins/visualizations/nvd3/nvd3_scatter/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_stackedarea/config/nvd3_stackedarea.xml
A config/plugins/visualizations/nvd3/nvd3_stackedarea/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/config/nvd3_stackedarea_full.xml
A config/plugins/visualizations/nvd3/nvd3_stackedarea_full/static/logo.png
A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/config/nvd3_stackedarea_stream.xml
A config/plugins/visualizations/nvd3/nvd3_stackedarea_stream/static/logo.png
A config/plugins/visualizations/phylocanvas/config/phylocanvas.xml
A config/plugins/visualizations/phylocanvas/package.json
A config/plugins/visualizations/phylocanvas/src/script.js
A config/plugins/visualizations/phylocanvas/static/logo.png
A config/plugins/visualizations/phylocanvas/static/script.js
A config/plugins/visualizations/pv/config/pv.xml
A config/plugins/visualizations/pv/package.json
A config/plugins/visualizations/pv/src/pv.js
A config/plugins/visualizations/pv/static/logo.png
A config/plugins/visualizations/pv/static/pv.js
M config/plugins/visualizations/scatterplot/config/scatterplot.xml
M config/plugins/visualizations/scatterplot/package.json
A config/plugins/visualizations/scatterplot/src/numeric-column-stats.js
M config/plugins/visualizations/scatterplot/src/scatterplot.js
A config/plugins/visualizations/scatterplot/src/worker-stats.js
A config/plugins/visualizations/scatterplot/static/8850628034555be072a0e4f882d4d8e5.js
R config/plugins/visualizations/scatterplot/static/numeric-column-stats.js
R config/plugins/visualizations/scatterplot/static/scatterplot.bundle.js
A config/plugins/visualizations/scatterplot/static/scatterplot.js
R config/plugins/visualizations/scatterplot/static/worker-stats.js
M config/plugins/visualizations/scatterplot/templates/scatterplot.mako
R config/plugins/visualizations/scatterplot/webpack.config.js
A config/plugins/visualizations/venn/config/venn.xml
A config/plugins/visualizations/venn/package.json
A config/plugins/visualizations/venn/src/script.js
A config/plugins/visualizations/venn/src/venn.js
A config/plugins/visualizations/venn/static/logo.png
A config/plugins/visualizations/venn/static/script.css
A config/plugins/visualizations/venn/static/script.js
M config/plugins/webhooks/demo/search/script.js
M config/reports.yml.sample
M config/tool_conf.xml.sample
M config/user_preferences_extra_conf.yml.sample
M doc/source/admin/galaxy_options.rst
M doc/source/admin/reports_options.rst
M doc/source/conf.py
A doc/source/conf.versioning.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam_native.xml
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/text.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/libraries.py
M lib/galaxy/managers/taggable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/model/mapping.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/views.py
M lib/galaxy/tools/execute.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/repositories.py
A lib/galaxy/tools/tag_collection_from_file.xml
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/galaxy/api/libraries.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/controllers/history.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/tool_shed/tools/tool_validator.py
M scripts/common_startup.sh
R static/scripts/packed
M static/style/blue/base.css
M templates/js-app.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/workflow/sharing.mako
A test-data/new_tags_1.txt
M test/api/test_visualizations.py
M test/base/interactor.py
A test/functional/tools/fail_writing_work_dir_file.xml
M test/functional/tools/samples_tool_conf.xml
M test/functional/twilltestcase.py
M test/selenium_tests/test_saved_histories.py
M test/unit/tools/test_tool_validation.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into history_structure
Commit: a847ce20965ecb6418b48616effb049c56568c01
https://github.com/galaxyproject/galaxy/commit/a847ce20965ecb6418b48616effb…
Author: Björn Grüning <bjoern(a)gruenings.eu>
Date: 2018-03-02 (Fri, 02 Mar 2018)
Changed paths:
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/extended.js
A client/galaxy/scripts/components/DisplayStructured.vue
A client/galaxy/scripts/components/HistoryView.vue
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
A lib/galaxy/util/create_history_template.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M static/style/blue/base.css
R templates/webapps/galaxy/history/display_structured.mako
R templates/webapps/galaxy/history/view.mako
Log Message:
-----------
Merge pull request #5317 from bgruening/history_structure
History structure
Compare: https://github.com/galaxyproject/galaxy/compare/de2bfa2ccacf...a847ce20965e
1
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01 Mar '18
Branch: refs/heads/usegalaxy
Home: https://github.com/galaxyproject/galaxy
Commit: bb19c7e44844bd724ba2ad3920abd078aae083a0
https://github.com/galaxyproject/galaxy/commit/bb19c7e44844bd724ba2ad3920ab…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-22 (Thu, 22 Feb 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam_native.xml
A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
A test-data/qname_sorted.bam
M test/functional/tools/sam_to_bam_native.xml
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Add queryname sorted and input sorted datatypes
The queryname sorted datatype (BamQuerynameSorted) ensures that the file is
queryname ordered. The BamInputSorted datatype can be used to describe the
output of aligners, which usually keep mate pairs adjacent. The BamInputSorted
datatype allows using tools that require mates to be adjacent, without
requiring an explicit sorting step. This can reduce the time and space
required for duplicate marking tools, HiC tools and structural variant
detection tools that require mates to be grouped together in an alignment file.
The BamQuerynameSorted has a converter that works for all datatypes that can be
consumed by samtools. There is no converter for BamInputSorted, since
BamQuerynameSorted is valid input for tools requiring BamInputSorted
input.
I'm targeting 18.01 since I think it would be very unfortunate if we start
annotating aligners with the very loose BamNative datatype, since this datatype
does not make any promises about sort order at all.
This closes https://github.com/galaxyproject/galaxy/issues/5497, goes
a long way towards the problems mentioned in https://github.com/galaxyproject/galaxy/issues/5496
and would make https://github.com/galaxyproject/tools-iuc/pull/1732 and https://github.com/galaxyproject/tools-iuc/pull/1591 better
Commit: 3dec3bdd21176d0fb66d7606a1e513ef244e4e86
https://github.com/galaxyproject/galaxy/commit/3dec3bdd21176d0fb66d7606a1e5…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Move `Extract genomic DNA 1` to list of version galaxy lib tools
Commit: 2d132a45d9af112a9d96e6a1d58646aff1a72910
https://github.com/galaxyproject/galaxy/commit/2d132a45d9af112a9d96e6a1d586…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #5626 from mvdbeek/limit_extract_dna_legacy_versions
[17.09] Move `Extract genomic DNA 1` to list of versioned galaxy tools requiring galaxy to be importable
Commit: 87c70d844747b6d99880e495be0102fe386ccdb0
https://github.com/galaxyproject/galaxy/commit/87c70d844747b6d99880e495be01…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge branch 'release_17.09' into release_18.01
Conflicts:
lib/galaxy/tools/__init__.py
Commit: d648e22080ac97b3940799d35e3be304d1a0aed7
https://github.com/galaxyproject/galaxy/commit/d648e22080ac97b3940799d35e3b…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/panel.py
Log Message:
-----------
fix for cases where panel elements have to_dict with different signature
we want to only cache Tools anyways, so this fixes other possible bug
where section/label etc would have same id as a Tool
change the detection of Tool object
to avoid circular import errors
Also use cache for dictifying sections, we should
gain more speed from that.
Commit: 5406a7153bd6a51174145d04eda26b6796211154
https://github.com/galaxyproject/galaxy/commit/5406a7153bd6a51174145d04eda2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/panel.py
Log Message:
-----------
pass the toolbox obj to make sure cache is available
Commit: b96fd2c74010009a7dc85c09e77f87a9d4eff271
https://github.com/galaxyproject/galaxy/commit/b96fd2c74010009a7dc85c09e77f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/panel.py
Log Message:
-----------
enable cache for tools that inherit from Tool
Commit: 77d085a40f5d5d2e131dc2fc8073e0c030599988
https://github.com/galaxyproject/galaxy/commit/77d085a40f5d5d2e131dc2fc8073…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam_native.xml
A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
A test-data/qname_sorted.bam
M test/functional/tools/sam_to_bam_native.xml
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Merge pull request #5589 from mvdbeek/samtools_queryname_and_input_order_datatypes
[18.01] Add queryname sorted and input sorted datatypes
Commit: 41910f824ea311e8ce7d93e4dc03a44c75c8132b
https://github.com/galaxyproject/galaxy/commit/41910f824ea311e8ce7d93e4dc03…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/panel.py
Log Message:
-----------
Merge pull request #5615 from martenson/distinct-elts
[18.01] fix for cases where panel elements have to_dict with different signature
Commit: 56b8ecd3d50340c366aa22d5327fd635a3485ff0
https://github.com/galaxyproject/galaxy/commit/56b8ecd3d50340c366aa22d5327f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-03-01 (Thu, 01 Mar 2018)
Changed paths:
M config/datatypes_conf.xml.sample
M lib/galaxy/datatypes/binary.py
R lib/galaxy/datatypes/converters/bam_native_to_bam_converter.xml
M lib/galaxy/datatypes/converters/sam_to_bam_native.xml
A lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
A lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/panel.py
A test-data/qname_sorted.bam
M test/functional/tools/sam_to_bam_native.xml
M test/functional/tools/sample_datatypes_conf.xml
Log Message:
-----------
Merge branch 'release_18.01' into usegalaxy
Compare: https://github.com/galaxyproject/galaxy/compare/ab928fe55ed1...56b8ecd3d503
1
0