Branch: refs/heads/usegalaxy Home: https://github.com/galaxyproject/galaxy Commit: f6ac13568f62731fb785e3aafafbf3aacf21a7a2 https://github.com/galaxyproject/galaxy/commit/f6ac13568f62731fb785e3aafafbf... Author: John Chilton jmchilton@gmail.com Date: 2018-02-18 (Sun, 18 Feb 2018)

Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js

Log Message: ----------- Don't fail rest of multi-action queue when attempting to purge a collection.

Fixes https://github.com/galaxyproject/galaxy/issues/5117.

Commit: 31e31e692311ba2e9f11d3eabe5253628f8e39c9 https://github.com/galaxyproject/galaxy/commit/31e31e692311ba2e9f11d3eabe525... Author: nekrut anton@nekrut.org Date: 2018-02-19 (Mon, 19 Feb 2018)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py

Log Message: ----------- added fasta.gz

Commit: d79717b86e0b6ecf5e540eb939888066b88081de https://github.com/galaxyproject/galaxy/commit/d79717b86e0b6ecf5e540eb939888... Author: nekrut anton@nekrut.org Date: 2018-02-19 (Mon, 19 Feb 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- fixed flake8 errors

Commit: 8cec1fd592a354be9b055fbb8b7f3ce72df39990 https://github.com/galaxyproject/galaxy/commit/8cec1fd592a354be9b055fbb8b7f3... Author: nekrut anton@nekrut.org Date: 2018-02-19 (Mon, 19 Feb 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- removing stray whitespace

Commit: d34524ff8adc694e41f0e582a57f705f2ed0dd7d https://github.com/galaxyproject/galaxy/commit/d34524ff8adc694e41f0e582a57f7... Author: nekrut anton@nekrut.org Date: 2018-02-19 (Mon, 19 Feb 2018)

Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml

Log Message: ----------- fixed name of fastagz->fasta converter

Commit: c4ce9695bbb577a0e9514c5cb71069156d33a943 https://github.com/galaxyproject/galaxy/commit/c4ce9695bbb577a0e9514c5cb7106... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-19 (Mon, 19 Feb 2018)

Changed paths: M lib/galaxy/datatypes/converters/fastagz_to_fasta.xml

Log Message: ----------- fix copypasta

Commit: 9feaf85585a30820dd71762431e1ed7d5b5c3b5e https://github.com/galaxyproject/galaxy/commit/9feaf85585a30820dd71762431e1e... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-19 (Mon, 19 Feb 2018)

Changed paths: M lib/galaxy/datatypes/sequence.py

Log Message: ----------- fix more fasta copypasta

Commit: 17a5d20278f7306e69e77054f92d976020e048ee https://github.com/galaxyproject/galaxy/commit/17a5d20278f7306e69e77054f92d9... Author: John Chilton jmchilton@gmail.com Date: 2018-02-19 (Mon, 19 Feb 2018)

Changed paths: M run_tests.sh

Log Message: ----------- In test framework only build client if running Selenium tests.

These shouldn't be required for any other test types I believe and it slows things down.

Commit: 6a3ce34c09bd516a18bd7d8f04851e1155d6d174 https://github.com/galaxyproject/galaxy/commit/6a3ce34c09bd516a18bd7d8f04851... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-19 (Mon, 19 Feb 2018)

Changed paths: M client/galaxy/scripts/mvc/history/history-view-edit.js

Log Message: ----------- Merge pull request #5443 from jmchilton/fix5117

[18.01] Don't silently fail rest of multi-action queue when attempting to purge a collection.

Commit: 2ca339d2b7cfdde817097837033e317a19b4a801 https://github.com/galaxyproject/galaxy/commit/2ca339d2b7cfdde817097837033e3... Author: Jelle Scholtalbers j.scholtalbers@gmail.com Date: 2018-02-20 (Tue, 20 Feb 2018)

Changed paths: M lib/galaxy/auth/__init__.py

Log Message: ----------- fix broken admin 'create new user' when registration =='challenge'

Commit: 01776c617b691c467e423c7a5f60c17be9b71503 https://github.com/galaxyproject/galaxy/commit/01776c617b691c467e423c7a5f60c... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-20 (Tue, 20 Feb 2018)

Changed paths: M lib/galaxy/auth/__init__.py

Log Message: ----------- Merge pull request #5569 from scholtalbers/fix/broken_create_new_user_challenge

[18.01] fix broken admin 'create new user' when registration =='challenge'

Commit: 99f7de456ce953f36e6122270209083fe443654b https://github.com/galaxyproject/galaxy/commit/99f7de456ce953f36e61222702090... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-20 (Tue, 20 Feb 2018)

Changed paths: M run_tests.sh

Log Message: ----------- Merge pull request #5566 from jmchilton/optimize_tests_0

[18.01] In test framework only build client if running Selenium tests.

Commit: 7715838dbbbcad980a47d1a96619b6e91fa7a623 https://github.com/galaxyproject/galaxy/commit/7715838dbbbcad980a47d1a96619b... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-20 (Tue, 20 Feb 2018)

Changed paths: M config/datatypes_conf.xml.sample A lib/galaxy/datatypes/converters/fastagz_to_fasta.xml M lib/galaxy/datatypes/sequence.py M lib/galaxy/datatypes/sniff.py

Log Message: ----------- Merge pull request #5561 from martenson/backport-fastgz

[18.01] add fasta.gz support

Commit: 93d5c54946e992112841df3461512bbeb6f5c7e9 https://github.com/galaxyproject/galaxy/commit/93d5c54946e992112841df3461512... Author: John Chilton jmchilton@gmail.com Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/web/framework/helpers/grids.py

Log Message: ----------- Optimize count query in grids (part 1).

Many grid operations execute a complex query twice - once to produce the total number of rows and once to iterate through the selected parts of the data. This can be more optimal in many ways - this starts us down the path to addressing that by doing two things.

The first thing it does is eliminates the query all together if paging is enabled but the user has opted to see "all" the rows. There was never a reason to execute the query in that case I don't think.

The second thing it does is move the calculation of the count query until after the data has been generated - this isn't more optimal by itself but it allows us to potentially calculate the count as part of the main query. I've implemented this in a broken way @ https://github.com/galaxyproject/galaxy/commit/ea404721585b5f78da1b91e57e31b... but I realized it was too broad an approach and doesn't work if certain kinds of joins are used in the initial query - but a more targetted approach on a per-grid basis could work I think and moving this code after allow us to potentially do that more easily in subsequent commits.

Additionally I added a note - that I think it would be best to just return None as the number of pages and issue a second query to the same endpoint with the same arguments but with count_only=true added as a query request parameter so we can render the main grid faster and then render the paging elements after the second query finishes. This would feel more responsive I think.

Commit: 1a782eb4eb29158a203df9e02b0195ecfe496e37 https://github.com/galaxyproject/galaxy/commit/1a782eb4eb29158a203df9e02b019... Author: John Chilton jmchilton@gmail.com Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Paginate published workflow grid.

@martenson mentioned he prefers the look and feel of the published history grid so this replicates that and very likely will result in quicker rendering on usegalaxy.org - though we should verify this after it is deployed since the paginated grid do result in two big join queries instead of one big query - but I suspect rendering details on fewer objects (which includes fetching tag information from the db) will saved more than enough to make up for that.

Commit: af0b40ea95c5244c58fbaa545b81ef4c4eff7cf0 https://github.com/galaxyproject/galaxy/commit/af0b40ea95c5244c58fbaa545b81e... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/web/proxy/js/package.json

Log Message: ----------- Bump sqlite3 dependency for web proxy

Commit: 5d422898582446575dfe30d13805c9e13a3f8104 https://github.com/galaxyproject/galaxy/commit/5d422898582446575dfe30d13805c... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/web/proxy/js/package.json

Log Message: ----------- Minor updates to commander, http-proxy. eventemitter3 is several major versions behind, needs testing before upgrade.

Commit: 1656c7b429854323efda82accc4c190a965be8a3 https://github.com/galaxyproject/galaxy/commit/1656c7b429854323efda82accc4c1... Author: John Chilton jmchilton@gmail.com Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py

Log Message: ----------- Fix repeated fetching dataset permissions in dynamic output collection.

Commit: b5b41d6172bd7e2894efcc3b423b11a37fb92823 https://github.com/galaxyproject/galaxy/commit/b5b41d6172bd7e2894efcc3b423b1... Author: Björn Grüning bjoern@gruenings.eu Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/web/proxy/js/package.json

Log Message: ----------- Merge pull request #5575 from dannon/web_proxy_fixes

[18.01] Bump sqlite3 dependency for web proxy

Commit: ff73cf2e6f8e1143e82681a9cfa97d769610f2c2 https://github.com/galaxyproject/galaxy/commit/ff73cf2e6f8e1143e82681a9cfa97... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Handle header-only bam files correctly indicating there is no more data to fetch when chunking

Commit: 34c5a1a1f39e4805b4b6e46d86e9db721c98199a https://github.com/galaxyproject/galaxy/commit/34c5a1a1f39e4805b4b6e46d86e9d... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Two minor linting issues (deprecated e.message, unused var)

Commit: 75b06187053de95f07fdbbb6caeaf3e52265238e https://github.com/galaxyproject/galaxy/commit/75b06187053de95f07fdbbb6caeaf... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M tools/data_source/upload.py

Log Message: ----------- Do not remove external path files during library uploads

xref. https://github.com/galaxyproject/galaxy/pull/5264#issuecomment-367172820

Commit: f7f9c120eda7f9d735257eecaeb759ad50473f57 https://github.com/galaxyproject/galaxy/commit/f7f9c120eda7f9d735257eecaeb75... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M test/integration/test_upload_configuration_options.py

Log Message: ----------- Refactor BaseFtpUploadConfigurationTestCase._write_ftp_file() method

Commit: f41230034689448abc6059d8e2771001961bafb9 https://github.com/galaxyproject/galaxy/commit/f41230034689448abc6059d8e2771... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- No need to str() it; %s does this -- thanks @nsoranzo

Commit: 117b4dcd6c503c51fb376c98ae8ba38d462d0301 https://github.com/galaxyproject/galaxy/commit/117b4dcd6c503c51fb376c98ae8ba... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M test/base/populators.py M test/integration/test_upload_configuration_options.py

Log Message: ----------- Update integration test to check external path files are not deleted after library upload

This test would have failed before commit 75b06187053de95f07fdbbb6caeaf3e52265238e.

Commit: c00e772159f6a121bc4f7759fa57f48e79c48f32 https://github.com/galaxyproject/galaxy/commit/c00e772159f6a121bc4f7759fa57f... Author: John Chilton jmchilton@gmail.com Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js

Log Message: ----------- Fix lack of feedback when slow grids are loading data from the server.

Fixes #5473 (after numerous other backend optimizations also).

Commit: 8afeffe95cc63832a6208e119cbfea4671a49a47 https://github.com/galaxyproject/galaxy/commit/8afeffe95cc63832a6208e119cbfe... Author: John Chilton jmchilton@gmail.com Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/datatypes/binary.py

Log Message: ----------- Merge pull request #5579 from dannon/fix_bam_nodata

[18.01] Fix small bam (header-only) infinite fetching

Commit: b861b9ad4d693000ba8cf492ce6b1ff057db3d34 https://github.com/galaxyproject/galaxy/commit/b861b9ad4d693000ba8cf492ce6b1... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/tools/toolbox/base.py

Log Message: ----------- implement basic cache on toolbox to_dict objects

base the cache on absence of filters

allow cache for users that don't opt in for filters

Commit: 8cc675eedd8bb895cf26cfc1fa5cbcc97e75f638 https://github.com/galaxyproject/galaxy/commit/8cc675eedd8bb895cf26cfc1fa5cb... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-21 (Wed, 21 Feb 2018)

Changed paths: M lib/galaxy/webapps/galaxy/controllers/workflow.py

Log Message: ----------- Merge pull request #5576 from jmchilton/workflow_paginate

[18.01] Paginate published workflows grid.

Commit: d9372739376f5d289740faae40e8790391d8d843 https://github.com/galaxyproject/galaxy/commit/d9372739376f5d289740faae40e87... Author: John Chilton jmchilton@gmail.com Date: 2018-02-22 (Thu, 22 Feb 2018)

Changed paths: M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py

Log Message: ----------- Merge pull request #5573 from nsoranzo/release_18.01_fix_filesystem_library_uploads

[18.01] Do not remove external path files during library uploads

Commit: 8806030f53c2b9d0002505bf5193be88d7cff8f9 https://github.com/galaxyproject/galaxy/commit/8806030f53c2b9d0002505bf5193b... Author: Nicola Soranzo nicola.soranzo@earlham.ac.uk Date: 2018-02-22 (Thu, 22 Feb 2018)

Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py

Log Message: ----------- Replace distutils.version with packaging.version

distutils under Python3 has this bug:

https://bugs.python.org/issue14894

which causes this traceback:

``` Traceback (most recent call last): File "lib/galaxy/webapps/galaxy/buildapp.py", line 49, in app_factory app = galaxy.app.UniverseApplication(global_conf=global_conf, **kwargs) File "lib/galaxy/app.py", line 125, in __init__ self._configure_toolbox() File "lib/galaxy/config.py", line 930, in _configure_toolbox self.toolbox = tools.ToolBox(tool_configs, self.config.tool_path, self) File "lib/galaxy/tools/__init__.py", line 232, in __init__ app=app, File "lib/galaxy/tools/toolbox/base.py", line 1056, in __init__ super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app) File "lib/galaxy/tools/toolbox/base.py", line 84, in __init__ self._load_tool_panel() File "lib/galaxy/tools/toolbox/base.py", line 358, in _load_tool_panel self.__add_tool_to_tool_panel(section_val, section, section=True) File "lib/galaxy/tools/toolbox/base.py", line 278, in __add_tool_to_tool_panel related_tool = self._lineage_in_panel(panel_dict, tool=tool) File "lib/galaxy/tools/toolbox/base.py", line 961, in _lineage_in_panel lineage_tool_versions = reversed(tool_lineage.get_versions()) File "lib/galaxy/tools/toolbox/lineages/interface.py", line 77, in get_versions return [ToolLineageVersion(tool_id, tool_version) for tool_id, tool_version in zip(self.tool_ids, self.tool_versions)] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 55, in tool_ids return ["%s/%s" % (tool_id, version) for version in self.tool_versions] File "lib/galaxy/tools/toolbox/lineages/interface.py", line 49, in tool_versions return sorted(self._tool_versions, key=LooseVersion) File "/usr/lib/python3.4/distutils/version.py", line 58, in __lt__ c = self._cmp(other) File "/usr/lib/python3.4/distutils/version.py", line 343, in _cmp if self.version < other.version: TypeError: unorderable types: str() < int() ```

when a tool version contains a letter in the "wrong" place (e.g. in the first position).

Fix https://github.com/galaxyproject/galaxy/issues/5408 .

Commit: ce3b40cfc10e134d5acc477757404eba40ea6553 https://github.com/galaxyproject/galaxy/commit/ce3b40cfc10e134d5acc477757404... Author: Marius van den Beek m.vandenbeek@gmail.com Date: 2018-02-22 (Thu, 22 Feb 2018)

Changed paths: M lib/galaxy/tools/parameters/output_collect.py

Log Message: ----------- Merge pull request #5578 from jmchilton/opt_dyn_collect

[18.01] Fix repeated fetching dataset permissions in dynamic output collection.

Commit: fc52fe5c62700b4f8527e4edead0fba4e7cfe33f https://github.com/galaxyproject/galaxy/commit/fc52fe5c62700b4f8527e4edead0f... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-22 (Thu, 22 Feb 2018)

Changed paths: M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py

Log Message: ----------- Merge pull request #5588 from jmchilton/backport_packaging

[18.01] Replace distutils.version with packaging.version

Commit: 8a88cb9827b68e6795cf00496008e1aa189185ad https://github.com/galaxyproject/galaxy/commit/8a88cb9827b68e6795cf00496008e... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-26 (Mon, 26 Feb 2018)

Changed paths: M lib/galaxy/tools/toolbox/base.py

Log Message: ----------- move the cache from toolbox level to tool level

the cache remains toolbox-specific so it is stored within the toolbox object

includes refactor thanks to eagle eyes

Commit: e3ced2c669485f76eae7fcfb3b32aa048730964d https://github.com/galaxyproject/galaxy/commit/e3ced2c669485f76eae7fcfb3b32a... Author: Dannon Baker dannon.baker@gmail.com Date: 2018-02-26 (Mon, 26 Feb 2018)

Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py

Log Message: ----------- Fix migration 0137's downgrade -- previously failed to select the correct column to drop

Commit: c8407786f25c98c87f441f15222f72eeea4edc72 https://github.com/galaxyproject/galaxy/commit/c8407786f25c98c87f441f15222f7... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-26 (Mon, 26 Feb 2018)

Changed paths: M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py

Log Message: ----------- Merge pull request #5605 from dannon/migrate_fix

[18.01] Fix migration 0137's downgrade

Commit: d8585f6a6f87735d072635495bd49047da746624 https://github.com/galaxyproject/galaxy/commit/d8585f6a6f87735d072635495bd49... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-27 (Tue, 27 Feb 2018)

Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js

Log Message: ----------- Merge pull request #5582 from jmchilton/indicators

[18.01] Fix lack of feedback when slow grids are loading data from the server.

Commit: 50cd159d4c212a36b8d3861295125ef055a296d9 https://github.com/galaxyproject/galaxy/commit/50cd159d4c212a36b8d3861295125... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-27 (Tue, 27 Feb 2018)

Changed paths: M lib/galaxy/web/framework/helpers/grids.py

Log Message: ----------- Merge pull request #5574 from jmchilton/optimize_count_query_1

[18.01] Optimize count query in grids (Part 1).

Commit: a90c3a1d3f2c2a12f285f3c21e91ca364f81853e https://github.com/galaxyproject/galaxy/commit/a90c3a1d3f2c2a12f285f3c21e91c... Author: John Chilton jmchilton@gmail.com Date: 2018-02-27 (Tue, 27 Feb 2018)

Changed paths: M lib/galaxy/tools/toolbox/base.py

Log Message: ----------- Merge pull request #5583 from martenson/backport-toolbox-cache

[18.01] Backport toolbox cache

Commit: ab928fe55ed1f871dbe6221e95af199579f312e1 https://github.com/galaxyproject/galaxy/commit/ab928fe55ed1f871dbe6221e95af1... Author: Martin Cech marten@bx.psu.edu Date: 2018-02-27 (Tue, 27 Feb 2018)

Changed paths: M client/galaxy/scripts/mvc/grid/grid-shared.js M client/galaxy/scripts/mvc/grid/grid-view.js M client/galaxy/scripts/mvc/history/history-list.js M client/galaxy/scripts/mvc/history/history-view-edit.js M client/galaxy/scripts/mvc/list/list-view.js M client/galaxy/scripts/mvc/workflow/workflow.js M client/galaxy/scripts/ui/loading-indicator.js M lib/galaxy/auth/__init__.py M lib/galaxy/datatypes/binary.py M lib/galaxy/datatypes/converters/sam_to_bam.py M lib/galaxy/dependencies/pinned-requirements.txt M lib/galaxy/dependencies/requirements.txt M lib/galaxy/jobs/runners/pulsar.py M lib/galaxy/model/migrate/versions/0137_add_copied_from_job_id_column.py M lib/galaxy/tools/__init__.py M lib/galaxy/tools/deps/conda_util.py M lib/galaxy/tools/deps/mulled/util.py M lib/galaxy/tools/parameters/output_collect.py M lib/galaxy/tools/toolbox/base.py M lib/galaxy/tools/toolbox/lineages/interface.py M lib/galaxy/visualization/data_providers/genome.py M lib/galaxy/web/framework/helpers/grids.py M lib/galaxy/web/proxy/js/package.json M lib/galaxy/webapps/galaxy/controllers/workflow.py M run_tests.sh M test/base/populators.py M test/integration/test_upload_configuration_options.py M tools/data_source/upload.py

Log Message: ----------- Merge branch 'release_18.01' into usegalaxy

Compare: https://github.com/galaxyproject/galaxy/compare/fa283b525f44...ab928fe55ed1