Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 9681ded30b087904005774435b2acc201a618a0a
https://github.com/galaxyproject/galaxy/commit/9681ded30b087904005774435b2a…
Author: Dave Bouvier <dave(a)bx.psu.edu>
Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
Log Message:
-----------
Improve handling of a missing R environment.
Previously, the error message 'Missing R environment. Please check
your specified R installation exists.' would be displayed in an
obscure location in the log. With this change, galaxy will set
the tool dependency to Error and display the error message in the
admin panel.
Commit: d0028bde0fee5a6158473a56ad357e942a92b7cb
https://github.com/galaxyproject/galaxy/commit/d0028bde0fee5a6158473a56ad35…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths:
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
Log Message:
-----------
Merge pull request #2215 from davebx/td_fix
Improve handling of a missing R environment.
Compare: https://github.com/galaxyproject/galaxy/compare/c563d37bfd8d...d0028bde0fee
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ca5f6053c7b13fa8f631f0a96f78a8aac544175c
https://github.com/galaxyproject/galaxy/commit/ca5f6053c7b13fa8f631f0a96f78…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M lib/galaxy/tools/__init__.py
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Fix tool action redirects for non-default tools displaying tool forms
Commit: f70a2b024237dcc797665134e311e7ada7602b1c
https://github.com/galaxyproject/galaxy/commit/f70a2b024237dcc797665134e311…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M lib/galaxy/tools/__init__.py
M static/maps/mvc/tool/tool-form.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form.js
Log Message:
-----------
Merge pull request #2211 from guerler/fix_nondefault_000
[16.04] Fix tool action redirect url for non-default tools
Commit: 971613404c68a3c3e8ee1ca8bc34693714c4ae17
https://github.com/galaxyproject/galaxy/commit/971613404c68a3c3e8ee1ca8bc34…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Avoid reset of cursor position for input fields during manual entry
Commit: 2734c2c4835ae725440c25314034f3dd296b00f1
https://github.com/galaxyproject/galaxy/commit/2734c2c4835ae725440c25314034…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Merge pull request #2218 from guerler/fix_cursor_001
[16.04] Avoid reset of cursor position for input fields during manual entry
Commit: c563d37bfd8da83fcd090067b32e3421b35802fb
https://github.com/galaxyproject/galaxy/commit/c563d37bfd8da83fcd090067b32e…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/tool/tool-form.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M lib/galaxy/tools/__init__.py
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Merge branch 'release_16.04' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/266a45ad7100...c563d37bfd8d
Branch: refs/heads/release_16.04
Home: https://github.com/galaxyproject/galaxy
Commit: 971613404c68a3c3e8ee1ca8bc34693714c4ae17
https://github.com/galaxyproject/galaxy/commit/971613404c68a3c3e8ee1ca8bc34…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Avoid reset of cursor position for input fields during manual entry
Commit: 2734c2c4835ae725440c25314034f3dd296b00f1
https://github.com/galaxyproject/galaxy/commit/2734c2c4835ae725440c25314034…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-21 (Thu, 21 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/ui/ui-misc.js
M static/maps/mvc/ui/ui-misc.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/ui/ui-misc.js
Log Message:
-----------
Merge pull request #2218 from guerler/fix_cursor_001
[16.04] Avoid reset of cursor position for input fields during manual entry
Compare: https://github.com/galaxyproject/galaxy/compare/f70a2b024237...2734c2c4835a
Branch: refs/heads/master
Home: https://github.com/galaxyproject/galaxy
Commit: 128a9112bb1635c1c49ac7dc1a99b531933ea659
https://github.com/galaxyproject/galaxy/commit/128a9112bb1635c1c49ac7dc1a99…
Author: MatthewRalston <mrals89(a)gmail.com>
Date: 2016-02-25 (Thu, 25 Feb 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
Checks for api_key before checking for header from SSO. Also fixes the NoneType issue discovered in #972.
Commit: 4e12c5e782249c3aea1ddbdd5bd2f363111e78b6
https://github.com/galaxyproject/galaxy/commit/4e12c5e782249c3aea1ddbdd5bd2…
Author: MatthewRalston <mrals89(a)gmail.com>
Date: 2016-02-25 (Thu, 25 Feb 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
Fixes NoneType problem in a simpler way. Thanks @nsoranzo.
Commit: 6473057f3b63ce615727800babbaf439ed66bb3f
https://github.com/galaxyproject/galaxy/commit/6473057f3b63ce615727800babba…
Author: Matt Ralston <mrals89(a)gmail.com>
Date: 2016-02-26 (Fri, 26 Feb 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
Adds whitespace
Commit: 774487ddcc9c0e793b6b15b26c971c3df5822644
https://github.com/galaxyproject/galaxy/commit/774487ddcc9c0e793b6b15b26c97…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-03-07 (Mon, 07 Mar 2016)
Changed paths:
M client/galaxy/scripts/mvc/citation/citation-model.js
M static/maps/mvc/citation/citation-model.js.map
M static/scripts/mvc/citation/citation-model.js
Log Message:
-----------
Fix citation-model to fail silently/gracefully when a non-parsable bibtex entry is tried
Commit: d225aebc8879b3e96963724d3b5b11aec1d50ed5
https://github.com/galaxyproject/galaxy/commit/d225aebc8879b3e96963724d3b5b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-03-07 (Mon, 07 Mar 2016)
Changed paths:
M client/galaxy/scripts/mvc/citation/citation-model.js
M static/maps/mvc/citation/citation-model.js.map
M static/scripts/mvc/citation/citation-model.js
Log Message:
-----------
Merge pull request #1884 from carlfeberhard/release_15.10
[15.10] Fix citation-model to fail silently/gracefully
Commit: e2a03646fd7c47a0ead962c9842e74f977dab8eb
https://github.com/galaxyproject/galaxy/commit/e2a03646fd7c47a0ead962c9842e…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-03-22 (Tue, 22 Mar 2016)
Changed paths:
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Fix farbtastic's use of deprecated jquery fns by loading jq-migrate in galaxy.panels.mako
Commit: 9cff686d6d94a8d4a47c4c5cdc9d380fe686a8c4
https://github.com/galaxyproject/galaxy/commit/9cff686d6d94a8d4a47c4c5cdc9d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-03-22 (Tue, 22 Mar 2016)
Changed paths:
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Merge pull request #1972 from carlfeberhard/release_15.10
[15.10] Fix farbtastic's use of deprecated jquery fns by loading jq-migrate i…
Commit: a2114fdd0e234a3253cec79a02e30899ca081359
https://github.com/galaxyproject/galaxy/commit/a2114fdd0e234a3253cec79a02e3…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-03-22 (Tue, 22 Mar 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
Merge pull request #1801 from MatthewRalston/api_key_patch
[15.10] Checks for api_key before checking for header from SSO.
Commit: 449098d8b14b45269be106f6410c0b9145c51d50
https://github.com/galaxyproject/galaxy/commit/449098d8b14b45269be106f6410c…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-03-30 (Wed, 30 Mar 2016)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
upgrade mercurial wheel to latest (fixing CVE issues)
Commit: dc4d4cbce7b18b33ff09f722d58a551c6f024b7a
https://github.com/galaxyproject/galaxy/commit/dc4d4cbce7b18b33ff09f722d58a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
M config/tool_shed.ini.sample
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
Log Message:
-----------
disable 'hg push' to TS repositories deprecated in 15.10 https://docs.galaxyproject.org/en/master/releases/15.10_announce.html#depre…
Commit: 7d08d1b0699a9e2adfa314af3e8324e257254ce0
https://github.com/galaxyproject/galaxy/commit/7d08d1b0699a9e2adfa314af3e83…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
Log Message:
-----------
Specify default value when getting disable_push
Commit: a560ad8999eca1137aafa466ae07683ef9f6d9d3
https://github.com/galaxyproject/galaxy/commit/a560ad8999eca1137aafa466ae07…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
A test/tool_shed/functional/test_0310_hg_clone.py
R test/tool_shed/functional/test_0310_hg_push_from_api.py
Log Message:
-----------
Update Tool Shed tests after disabling 'hg push'
Commit: 28b5dd36832642b5ae519790c25fc2d15da11ca9
https://github.com/galaxyproject/galaxy/commit/28b5dd36832642b5ae519790c25f…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
M test/tool_shed/base/twilltestcase.py
M test/tool_shed/functional/test_0310_hg_clone.py
Log Message:
-----------
add TS test for disabled hg push
Commit: 0bcc7e37e1d94259c6b5c29ab7e8041e4228d05d
https://github.com/galaxyproject/galaxy/commit/0bcc7e37e1d94259c6b5c29ab7e8…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
A test/tool_shed/functional/test_0310_hg_api_features.py
R test/tool_shed/functional/test_0310_hg_clone.py
Log Message:
-----------
rename test to reflect insides
Commit: 193eeaa60674eaa1badb65f74cb77dcb331b179b
https://github.com/galaxyproject/galaxy/commit/193eeaa60674eaa1badb65f74cb7…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
M config/tool_shed.ini.sample
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M test/tool_shed/base/twilltestcase.py
A test/tool_shed/functional/test_0310_hg_api_features.py
R test/tool_shed/functional/test_0310_hg_push_from_api.py
Log Message:
-----------
Merge pull request #2056 from martenson/1601-disable-push
[16.01] retroactively disable Mercurial push API in TS
Commit: 90b95dc665bd736a21bd16d2852caf5c23bb83c4
https://github.com/galaxyproject/galaxy/commit/90b95dc665bd736a21bd16d2852c…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2016-03-31 (Thu, 31 Mar 2016)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Merge pull request #2043 from martenson/update_mercurial_wheel
[16.01] upgrade mercurial wheel to latest (fixing CVE issues)
Commit: 20f61e6a2f36967e16a92cbcf8ad7f81ca76fb29
https://github.com/galaxyproject/galaxy/commit/20f61e6a2f36967e16a92cbcf8ad…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-04-04 (Mon, 04 Apr 2016)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
workaround for error message in case original toolshed had been disabled
Commit: 65a7ebee23364a89d72e528bfcde6b1f6b3c5cd9
https://github.com/galaxyproject/galaxy/commit/65a7ebee23364a89d72e528bfcde…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-04 (Mon, 04 Apr 2016)
Changed paths:
M lib/galaxy/workflow/modules.py
Log Message:
-----------
Merge pull request #2072 from mvdbeek/backport_1738
[16.01] backport #1738
Commit: 2a53be67ad4ac99b6e9fe5fb803bfa44442dbd3c
https://github.com/galaxyproject/galaxy/commit/2a53be67ad4ac99b6e9fe5fb803b…
Author: guerler <aysam.guerler(a)gmail.com>
Date: 2016-04-05 (Tue, 05 Apr 2016)
Changed paths:
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Show sections in workflow run
Commit: 3002e404ef17cd7db9b817085b2f3ed5a82bd109
https://github.com/galaxyproject/galaxy/commit/3002e404ef17cd7db9b817085b2f…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-04-05 (Tue, 05 Apr 2016)
Changed paths:
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Patch in visual separation of section parameters
Commit: 040410b1d3f0ea01374f183ee0b9447e0fc3cefb
https://github.com/galaxyproject/galaxy/commit/040410b1d3f0ea01374f183ee0b9…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-05 (Tue, 05 Apr 2016)
Changed paths:
M templates/webapps/galaxy/workflow/run.mako
Log Message:
-----------
Merge pull request #2092 from erasche/workflow-section-backport
[16.01] Workflow section fix backport
Commit: 9ecf99c227466a586a6299e37555655f5ff79a25
https://github.com/galaxyproject/galaxy/commit/9ecf99c227466a586a6299e37555…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-06 (Wed, 06 Apr 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
make dependencies browsable again
it would be denied previously as the dependency folder is
outside of the repository (symlink protection)
Commit: 0882b4d8fb31752f1fa8c963c3f260f975c918f7
https://github.com/galaxyproject/galaxy/commit/0882b4d8fb31752f1fa8c963c3f2…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-06 (Wed, 06 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/repository.py
Log Message:
-----------
use proper method for detecting admin
Commit: 50268cb8ca4a5f812346a71cc640141781f22a3d
https://github.com/galaxyproject/galaxy/commit/50268cb8ca4a5f812346a71cc640…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-07 (Thu, 07 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
fix missing call; add docs and refactor a bit
Commit: 455113d182236a0fec880db296b746a413a8edc4
https://github.com/galaxyproject/galaxy/commit/455113d182236a0fec880db296b7…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-04-08 (Fri, 08 Apr 2016)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/tool_shed/util/shed_util_common.py
Log Message:
-----------
Merge pull request #2101 from martenson/fix-browsing-dependencies
[16.01] make dependencies browsable again
Commit: f759961a29eeb28c6140d5d206bfd93fbdbfd379
https://github.com/galaxyproject/galaxy/commit/f759961a29eeb28c6140d5d206bf…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-11 (Mon, 11 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
Log Message:
-----------
mention planemo in the error message for disabled TS pushing
rephrase to Norwegian
Commit: fe4afefc42a45faca09c7c2aea34a97cad02be76
https://github.com/galaxyproject/galaxy/commit/fe4afefc42a45faca09c7c2aea34…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-04-11 (Mon, 11 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
Log Message:
-----------
Merge pull request #2114 from martenson/planemo-mention
[16.01] mention planemo in the error message for disabled TS pushing
Commit: cde04ad52d40b5d7b26a0c636d9d24bf6adbdc92
https://github.com/galaxyproject/galaxy/commit/cde04ad52d40b5d7b26a0c636d9d…
Author: Nicola Soranzo <nicola.soranzo(a)tgac.ac.uk>
Date: 2016-04-12 (Tue, 12 Apr 2016)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
-----------
markupsafe.escape() in Python2 does not work on str containing non-ASCII characters.
Fix #2135.
Commit: 2ebe9405106dfc16504e3b6f775425634bb4691f
https://github.com/galaxyproject/galaxy/commit/2ebe9405106dfc16504e3b6f7754…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-12 (Tue, 12 Apr 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
load options from config, not from options
Commit: ad952a4b8d7501d0df48e44d7c966ff22f9a63c4
https://github.com/galaxyproject/galaxy/commit/ad952a4b8d7501d0df48e44d7c96…
Author: carlfeberhard <carlfeberhard(a)users.noreply.github.com>
Date: 2016-04-12 (Tue, 12 Apr 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Merge pull request #2139 from martenson/fix-inactivity
[16.01] load options from config, not from options
Commit: 1e3b3a15581ecd62e78999f6be9e74d9e7cfbc65
https://github.com/galaxyproject/galaxy/commit/1e3b3a15581ecd62e78999f6be9e…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-12 (Tue, 12 Apr 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
fix the value passed to Masthead as options were options.config before
Commit: 4c2bca51171efff42e2852bfa59a91d5acee3e73
https://github.com/galaxyproject/galaxy/commit/4c2bca51171efff42e2852bfa59a…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M static/maps/layout/page.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
Log Message:
-----------
Merge pull request #2141 from martenson/fix-sideeffect
[16.01] fix the value passed to Masthead as options were options.config before
Commit: f85aaa4a27a1067a108c05fd1f74fa6060aa4565
https://github.com/galaxyproject/galaxy/commit/f85aaa4a27a1067a108c05fd1f74…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-13 (Wed, 13 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/buildapp.py
Log Message:
-----------
port of middleware fix for TS (#2106)
Commit: c0d65092fbbd1ad7380a0b17d3d9a949145d6170
https://github.com/galaxyproject/galaxy/commit/c0d65092fbbd1ad7380a0b17d3d9…
Author: Nicola Soranzo <nsoranzo(a)tiscali.it>
Date: 2016-04-14 (Thu, 14 Apr 2016)
Changed paths:
M lib/galaxy/webapps/tool_shed/buildapp.py
Log Message:
-----------
Merge pull request #2154 from martenson/port-middleware-fix
[16.01] Port middleware fix
Commit: 03c85737319dbce1a3c9aa258c7c22d2d97d5c35
https://github.com/galaxyproject/galaxy/commit/03c85737319dbce1a3c9aa258c7c…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-04-14 (Thu, 14 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/multi-panel.js
M static/maps/mvc/history/multi-panel.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/multi-panel.js
Log Message:
-----------
Multi-history: open rerun button in new tab
Commit: e26bff23ed05eeeb7bac469b95a4ee6509dd537c
https://github.com/galaxyproject/galaxy/commit/e26bff23ed05eeeb7bac469b95a4…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-04-14 (Thu, 14 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/citation/citation-model.js
M lib/galaxy/web/framework/middleware/remoteuser.py
M static/maps/mvc/citation/citation-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/citation/citation-model.js
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Merge 'release_15.10' with 'release_16.01'
Commit: 570baa5bb6020a2a8b7592dda8e952225ce7beec
https://github.com/galaxyproject/galaxy/commit/570baa5bb6020a2a8b7592dda8e9…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-04-14 (Thu, 14 Apr 2016)
Changed paths:
M lib/galaxy/web/framework/middleware/remoteuser.py
Log Message:
-----------
Fix bad merge: when HTTP_GX_SECRET is None
Commit: 68ce6ce49cc8c3d6f252a52a6bf9ac90f64328a3
https://github.com/galaxyproject/galaxy/commit/68ce6ce49cc8c3d6f252a52a6bf9…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-14 (Thu, 14 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/citation/citation-model.js
M lib/galaxy/web/framework/middleware/remoteuser.py
M static/maps/mvc/citation/citation-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/citation/citation-model.js
M templates/webapps/galaxy/galaxy.panels.mako
Log Message:
-----------
Merge pull request #2169 from carlfeberhard/release_16.01
[16.01] Merge 15.10 with 16.01
Commit: 18c00899a30cd162cd0bb3a251a49cff2143d3a3
https://github.com/galaxyproject/galaxy/commit/18c00899a30cd162cd0bb3a251a4…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-14 (Thu, 14 Apr 2016)
Changed paths:
M lib/galaxy/web/framework/helpers/grids.py
Log Message:
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Merge pull request #2138 from nsoranzo/release_16.01_fix_for_2135
[16.01] markupsafe.escape() in Python2 does not work on str containing non-ASCII characters
Commit: e193e46e30d84d7f844a2941f72ed65af11f69b3
https://github.com/galaxyproject/galaxy/commit/e193e46e30d84d7f844a2941f72e…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Place $headers before integrity_check
PBS needs the resource selection (which will be filled in using $headers) to
appear before anything else (except the shebang), so this changes the order.
Commit: 434321915a61f53cd668170da076251a8c15889f
https://github.com/galaxyproject/galaxy/commit/434321915a61f53cd668170da076…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
Log Message:
-----------
Use "$NCPUS" if defined to set GALAXY_SLOTS
On our PBS cluster we do not have $PBS_NCPUS, and $PBS_NODEFILE contains the
hostname of the nodes the task runs on. But we do have "$NCPUS" with the
correct number of CPUS.
Commit: 8e72b3095bacdac90a6fa7dea6125f489826bcfd
https://github.com/galaxyproject/galaxy/commit/8e72b3095bacdac90a6fa7dea612…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
Log Message:
-----------
Merge pull request #2174 from mvdbeek/reorder_job_template
[16.01] Backport #2146 #2145
Commit: 3e79a574bea53731c734b568e1c6eeab4199cbdd
https://github.com/galaxyproject/galaxy/commit/3e79a574bea53731c734b568e1c6…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/history/multi-panel.js
M static/maps/mvc/history/multi-panel.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/history/multi-panel.js
Log Message:
-----------
Merge #2167 manually to resolve conflicts.
Commit: 9e278de3959200a1432cca6ba33bc6e7ddd89b60
https://github.com/galaxyproject/galaxy/commit/9e278de3959200a1432cca6ba33b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Rebuild client.
Commit: b95cca862cae9cf7e78370fd68ea5f530fb8194f
https://github.com/galaxyproject/galaxy/commit/b95cca862cae9cf7e78370fd68ea…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-15 (Fri, 15 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-library-view.js
Log Message:
-----------
always fetch new permissions as we are reusing the view
Commit: e2f88296f8454e9195ad1a6f2d4c9c9ade40ee77
https://github.com/galaxyproject/galaxy/commit/e2f88296f8454e9195ad1a6f2d4c…
Author: Eric Rasche <rasche.eric(a)gmail.com>
Date: 2016-04-18 (Mon, 18 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-library-view.js
Log Message:
-----------
Merge pull request #2176 from martenson/fix-permissions-caching
[16.01] libraries: always fetch new permissions as we are reusing the view
Commit: cfb8ed32693d6aad0ef26af7af7171e0e8c3ee04
https://github.com/galaxyproject/galaxy/commit/cfb8ed32693d6aad0ef26af7af71…
Author: carlfeberhard <carlfeberhard(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/citation/citation-model.js
M static/maps/mvc/citation/citation-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/citation/citation-model.js
Log Message:
-----------
UI, citations: fix bad merge from 15.10
774487d created a difference between the imported name and the one
used.
Commit: 3737fc9487ad25ba09960e0d7858d4c15a3087bf
https://github.com/galaxyproject/galaxy/commit/3737fc9487ad25ba09960e0d7858…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-19 (Tue, 19 Apr 2016)
Changed paths:
M client/galaxy/scripts/mvc/citation/citation-model.js
M static/maps/mvc/citation/citation-model.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/mvc/citation/citation-model.js
Log Message:
-----------
Merge pull request #2198 from carlfeberhard/fix.citations-again
[16.01] UI, citations: fix bad merge from 15.10
Commit: ebb49d460b7cb5573a34cc386502a66594f8e3ad
https://github.com/galaxyproject/galaxy/commit/ebb49d460b7cb5573a34cc386502…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2016-04-20 (Wed, 20 Apr 2016)
Changed paths:
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Make client, somehow this got out of sync.
Commit: 5aefe1b193d866185958645b832f2d731f933c01
https://github.com/galaxyproject/galaxy/commit/5aefe1b193d866185958645b832f…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-20 (Wed, 20 Apr 2016)
Changed paths:
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js.map
Log Message:
-----------
Merge pull request #2207 from dannon/release_16.01
[16.01] Rebuild client, maps were out of sync.
Commit: b79474083b08860923f7f28fc1e7442b53f925db
https://github.com/galaxyproject/galaxy/commit/b79474083b08860923f7f28fc1e7…
Author: Martin Cech <cech.marten(a)gmail.com>
Date: 2016-04-20 (Wed, 20 Apr 2016)
Changed paths:
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/library/library-dataset-view.js
M client/galaxy/scripts/mvc/library/library-folder-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M config/tool_shed.ini.sample
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/tool_shed/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/webapps/tool_shed/controllers/repository.py
M lib/galaxy/webapps/tool_shed/framework/middleware/hg.py
M lib/galaxy/workflow/modules.py
M lib/tool_shed/util/shed_util_common.py
M static/maps/layout/page.js.map
M static/maps/mvc/citation/citation-model.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/library/library-dataset-view.js.map
M static/maps/mvc/library/library-folder-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/scripts/bundled/analysis.bundled.js
M static/scripts/bundled/analysis.bundled.js.map
M static/scripts/bundled/libs.bundled.js
M static/scripts/bundled/libs.bundled.js.map
M static/scripts/layout/page.js
M static/scripts/mvc/citation/citation-model.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/library/library-dataset-view.js
M static/scripts/mvc/library/library-folder-view.js
M static/scripts/mvc/library/library-library-view.js
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/workflow/run.mako
M test/tool_shed/base/twilltestcase.py
A test/tool_shed/functional/test_0310_hg_api_features.py
R test/tool_shed/functional/test_0310_hg_push_from_api.py
Log Message:
-----------
Merge pull request #2206 from dannon/master
Sanity check of master update.
Compare: https://github.com/galaxyproject/galaxy/compare/7c94ac8d93b8...b79474083b08