Branch: refs/heads/usegalaxy
Home: https://github.com/galaxyproject/galaxy
Commit: 62ee8e8404fb86155d9893a8eeab1cf58473d795
https://github.com/galaxyproject/galaxy/commit/62ee8e8404fb86155d9893a8eeab…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-17 (Fri, 17 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Fix Python environment hack to allow "fixing" tool ids at some version.
This is a less broken alternative to #3620 and something I intended to ultimately do anyway.
sam-to-bam used to be broken but now it isn't, we need to express that. Ideally we would move most of the things from the unversioned list to the versioned list as they are fixed.
xref https://github.com/galaxyproject/galaxy/pull/3620#issuecomment-280674067
xref https://github.com/galaxyproject/galaxy/commit/fe2a1d8ade4fbda158ae035c7813…
xref #3351
xref galaxyproject/tools-iuc#1148
Commit: eb6c0e410e600171fa3ce4fffb78bc205aad5292
https://github.com/galaxyproject/galaxy/commit/eb6c0e410e600171fa3ce4fffb78…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-17 (Fri, 17 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Rework preserve python environment expression according to :eagle::eyes: suggestion.
https://github.com/galaxyproject/galaxy/pull/3630#discussion_r101798306
Commit: 6733c36318bacce0bbf33a8d266f6a08de3ba019
https://github.com/galaxyproject/galaxy/commit/6733c36318bacce0bbf33a8d266f…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
[17.01] Restore logging statement missing when resolve_all is used.
Broken in #3391.
Commit: 49ef352235f7c998e79ca5423fab9725ea28d8be
https://github.com/galaxyproject/galaxy/commit/49ef352235f7c998e79ca5423fab…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/tools/deps/__init__.py
Log Message:
-----------
Merge pull request #3646 from jmchilton/resolve_all_logging
[17.01] Restore logging statement missing when resolve_all is used.
Commit: 9ebe2d2dd6efde7a66c52681aa57c52342ad992d
https://github.com/galaxyproject/galaxy/commit/9ebe2d2dd6efde7a66c52681aa57…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
Log Message:
-----------
Merge pull request #3630 from jmchilton/python_hack_scalpel
[17.01] Fix Python environment hack to allow "fixing" tool ids at some version.
Commit: 90de3f2588a61382e70b6209ea39293c6a3987f1
https://github.com/galaxyproject/galaxy/commit/90de3f2588a61382e70b6209ea39…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/version.py
Log Message:
-----------
Update version to 17.01
Commit: d10f740cff8e3520383c004a16830700b2789c9f
https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a1683…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
A templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
The user controller functions for changing information were ripped out before providing a way for admin functionality to use the new javascript stuff. Seems nontrivial, so this puts the endpoint back temporarily until the adminjs rewrite which can include the new functionality.
Commit: 6f3c8c7447e9a71c580ef9307395cd5dcd314915
https://github.com/galaxyproject/galaxy/commit/6f3c8c7447e9a71c580ef9307395…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
This template inherited field never worked apparently, but nobody noticed. This correctly sets the is_admin flag here.
Commit: 4be00d3058396ed30da4f6f0958ad6fa989249cb
https://github.com/galaxyproject/galaxy/commit/4be00d3058396ed30da4f6f0958a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Strip out unnecessary user address editing.
Commit: 456acf0b84004c85c94d3129f0a89af9be2d5452
https://github.com/galaxyproject/galaxy/commit/456acf0b84004c85c94d3129f0a8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Update docstring to explicitly mention this as a temporary endpoint.
Commit: b46ac475a93fbf0da71272861677a00a3877b91b
https://github.com/galaxyproject/galaxy/commit/b46ac475a93fbf0da71272861677…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Fix verbiage in temporary method.
Commit: 64036a441284151e1b1a3e9305537d526005ff3a
https://github.com/galaxyproject/galaxy/commit/64036a441284151e1b1a3e930553…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
A templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Merge pull request #3656 from dannon/admin-userinfo-edit-fix
[17.01] Admin user information editing
Commit: a352b3c490c7f5d7fbcf4e28a129bc8a537d3b53
https://github.com/galaxyproject/galaxy/commit/a352b3c490c7f5d7fbcf4e28a129…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/version.py
M lib/galaxy/webapps/galaxy/controllers/user.py
A templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Merge branch 'release_17.01' into usegalaxy
Compare: https://github.com/galaxyproject/galaxy/compare/277c4ed20bdf...a352b3c490c7
Branch: refs/heads/release_17.01
Home: https://github.com/galaxyproject/galaxy
Commit: d10f740cff8e3520383c004a16830700b2789c9f
https://github.com/galaxyproject/galaxy/commit/d10f740cff8e3520383c004a1683…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
A templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
The user controller functions for changing information were ripped out before providing a way for admin functionality to use the new javascript stuff. Seems nontrivial, so this puts the endpoint back temporarily until the adminjs rewrite which can include the new functionality.
Commit: 6f3c8c7447e9a71c580ef9307395cd5dcd314915
https://github.com/galaxyproject/galaxy/commit/6f3c8c7447e9a71c580ef9307395…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
This template inherited field never worked apparently, but nobody noticed. This correctly sets the is_admin flag here.
Commit: 4be00d3058396ed30da4f6f0958ad6fa989249cb
https://github.com/galaxyproject/galaxy/commit/4be00d3058396ed30da4f6f0958a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Strip out unnecessary user address editing.
Commit: 456acf0b84004c85c94d3129f0a89af9be2d5452
https://github.com/galaxyproject/galaxy/commit/456acf0b84004c85c94d3129f0a8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Update docstring to explicitly mention this as a temporary endpoint.
Commit: b46ac475a93fbf0da71272861677a00a3877b91b
https://github.com/galaxyproject/galaxy/commit/b46ac475a93fbf0da71272861677…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
Log Message:
-----------
Fix verbiage in temporary method.
Commit: 64036a441284151e1b1a3e9305537d526005ff3a
https://github.com/galaxyproject/galaxy/commit/64036a441284151e1b1a3e930553…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/user.py
A templates/webapps/galaxy/user/manage_info.mako
Log Message:
-----------
Merge pull request #3656 from dannon/admin-userinfo-edit-fix
[17.01] Admin user information editing
Compare: https://github.com/galaxyproject/galaxy/compare/90de3f2588a6...64036a441284
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8130d8b4c88343cdd44243fe700eae3fb863cc1a
https://github.com/galaxyproject/galaxy/commit/8130d8b4c88343cdd44243fe700e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-02-22 (Wed, 22 Feb 2017)
Changed paths:
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Update against the latest changes in galaxy-dev.
Commit: 99fdc37b815ab9c26f15250d722f2d30ab9691b2
https://github.com/galaxyproject/galaxy/commit/99fdc37b815ab9c26f15250d722f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-02-23 (Thu, 23 Feb 2017)
Changed paths:
M lib/galaxy/exceptions/error_codes.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/mulled/invfile.lua
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/linters/general.py
M lib/galaxy/tools/linters/outputs.py
M lib/galaxy/tools/linters/stdio.py
M lib/galaxy/tools/linters/tests.py
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Merge pull request #3654 from jmchilton/galaxy-lib-update
Update against the latest changes in galaxy-lib
Compare: https://github.com/galaxyproject/galaxy/compare/647fcad924a9...99fdc37b815a