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November 2017
- 1 participants
- 160 discussions
[galaxyproject/galaxy] b978ac: Revert "Remove downloading workflows through contr...
by GitHub 13 Nov '17
by GitHub 13 Nov '17
13 Nov '17
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: b978acbe62053596e5c2ae736c848a62dc936591
https://github.com/galaxyproject/galaxy/commit/b978acbe62053596e5c2ae736c84…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-12 (Sun, 12 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Revert "Remove downloading workflows through controller"
This reverts commit 1a4effa70e9ad8088e19ae334753b7a898d286aa.
This is used when downloading workflows with the save icom from "pages".
Commit: 3b523260551d15241de5dce3d1023790dcfd2250
https://github.com/galaxyproject/galaxy/commit/3b523260551d15241de5dce3d102…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/webapps/galaxy/controllers/workflow.py
Log Message:
-----------
Merge pull request #4988 from jmchilton/revert_export_to_file
[17.09] Revert export to file
Compare: https://github.com/galaxyproject/galaxy/compare/577d57a69ce0...3b523260551d
1
0
13 Nov '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b7e05a012cb8dd3bf90f31f5c5a7df44587e97c0
https://github.com/galaxyproject/galaxy/commit/b7e05a012cb8dd3bf90f31f5c5a7…
Author: Ignacio Eguinoa <igegu(a)psb.ugent.be>
Date: 2017-11-01 (Wed, 01 Nov 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
otherwise it will overwrite linking source file
Commit: 19e5478cb8ffbd9d97db663bb1d04e52bed721a0
https://github.com/galaxyproject/galaxy/commit/19e5478cb8ffbd9d97db663bb1d0…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-02 (Thu, 02 Nov 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Merge pull request #4911 from jmchilton/backport_4858
[17.09] Backport #4858
Commit: e3be7c31d59b69571bcee04599bdac6693426b89
https://github.com/galaxyproject/galaxy/commit/e3be7c31d59b69571bcee04599bd…
Author: Wolfgang Maier <wolfgang.maier(a)biologie.uni-freiburg.de>
Date: 2017-11-03 (Fri, 03 Nov 2017)
Changed paths:
M doc/source/releases/17.09_announce.rst
Log Message:
-----------
fix broken link in 17.09 announcement
Commit: 222ece4eabb6d080c6b8a0e327f8cf617b8a194f
https://github.com/galaxyproject/galaxy/commit/222ece4eabb6d080c6b8a0e327f8…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-03 (Fri, 03 Nov 2017)
Changed paths:
M doc/source/releases/17.09_announce.rst
Log Message:
-----------
Merge pull request #4927 from wm75/patch-2
fix broken link in 17.09 announcement
Commit: b6a0a1b084fe09de394aa6d0fb3caabc9fdf98a3
https://github.com/galaxyproject/galaxy/commit/b6a0a1b084fe09de394aa6d0fb3c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-11 (Sat, 11 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Tolerate IOError in tool and data table watcher
Without these changes the watcher thread may die when manually deleting loc files:
```
Exception in thread Thread-7:
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 199, in run
self.dispatch_events(self.event_queue, self.timeout)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 368, in dispatch_events
handler.dispatch(event)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/events.py", line 322, in dispatch
self.on_any_event(event)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 226, in on_any_event
self._handle(event)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 235, in _handle
cur_hash = md5_hash_file(path)
File "/Users/mvandenb/src/galaxy/lib/galaxy/util/hash_util.py", line 23, in md5_hash_file
with open(path, 'rb') as afile:
IOError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc'
```
Similar problems could occur when deleting tool xml files.
Commit: 231ce40e8154bd44fc1e5a0072489b9b81ad5377
https://github.com/galaxyproject/galaxy/commit/231ce40e8154bd44fc1e5a007248…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-12 (Sun, 12 Nov 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Encode file content with utf-8
There shouldn't be any disadvantages over doing this only for specific elements.
This also fixes https://github.com/galaxyproject/galaxy/issues/4345#issuecomment-343753378.
I have tested this with unicode strings in the name and info fields.
Commit: 0c9b42035bc51d6a66f5a6e0746fd28c67996cb3
https://github.com/galaxyproject/galaxy/commit/0c9b42035bc51d6a66f5a6e0746f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Open files in text-mode (thx @nsoranzo)
Commit: 6915007f85482648999768eecb9920da57b42e59
https://github.com/galaxyproject/galaxy/commit/6915007f85482648999768eecb99…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Merge pull request #4981 from mvdbeek/watcher_error_delete
[17.05][BUG] Tolerate IOError in tool and data table watcher
Commit: a0b4a2de53793c85a9b0443be4b2e4a8f4421759
https://github.com/galaxyproject/galaxy/commit/a0b4a2de53793c85a9b0443be4b2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Merge pull request #4987 from mvdbeek/history_import_bug
[17.09][Bug] Encode file content with utf-8
Commit: 577d57a69ce0d6d7f7c60ebc98009443cae204a0
https://github.com/galaxyproject/galaxy/commit/577d57a69ce0d6d7f7c60ebc9800…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Merge branch 'release_17.05' into release_17.09
Commit: e78efe16f4325a8abb7701fc62b5969ef89781db
https://github.com/galaxyproject/galaxy/commit/e78efe16f4325a8abb7701fc62b5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M doc/source/releases/17.09_announce.rst
M lib/galaxy/tools/cache.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Merge branch 'release_17.09' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/a18835b5169c...e78efe16f432
1
0
13 Nov '17
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: b6a0a1b084fe09de394aa6d0fb3caabc9fdf98a3
https://github.com/galaxyproject/galaxy/commit/b6a0a1b084fe09de394aa6d0fb3c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-11 (Sat, 11 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Tolerate IOError in tool and data table watcher
Without these changes the watcher thread may die when manually deleting loc files:
```
Exception in thread Thread-7:
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 199, in run
self.dispatch_events(self.event_queue, self.timeout)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 368, in dispatch_events
handler.dispatch(event)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/events.py", line 322, in dispatch
self.on_any_event(event)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 226, in on_any_event
self._handle(event)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 235, in _handle
cur_hash = md5_hash_file(path)
File "/Users/mvandenb/src/galaxy/lib/galaxy/util/hash_util.py", line 23, in md5_hash_file
with open(path, 'rb') as afile:
IOError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc'
```
Similar problems could occur when deleting tool xml files.
Commit: 6915007f85482648999768eecb9920da57b42e59
https://github.com/galaxyproject/galaxy/commit/6915007f85482648999768eecb99…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Merge pull request #4981 from mvdbeek/watcher_error_delete
[17.05][BUG] Tolerate IOError in tool and data table watcher
Commit: 577d57a69ce0d6d7f7c60ebc98009443cae204a0
https://github.com/galaxyproject/galaxy/commit/577d57a69ce0d6d7f7c60ebc9800…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Merge branch 'release_17.05' into release_17.09
Compare: https://github.com/galaxyproject/galaxy/compare/a0b4a2de5379...577d57a69ce0
1
0
[galaxyproject/galaxy] cb01f3: Create the $GALAXY_MEMORY_MB tool job environment ...
by GitHub 13 Nov '17
by GitHub 13 Nov '17
13 Nov '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: cb01f3dd332c4ff1b6a5e1ffff53a3758b8ac15e
https://github.com/galaxyproject/galaxy/commit/cb01f3dd332c4ff1b6a5e1ffff53…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-08 (Wed, 08 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Create the $GALAXY_MEMORY_MB tool job environment variable and attempt
to set it automatically under Slurm.
Commit: 49c0c406e5f386307c20b190844a25fd41974a73
https://github.com/galaxyproject/galaxy/commit/49c0c406e5f386307c20b190844a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-10 (Fri, 10 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
Log Message:
-----------
When setting $GALAXY_MEMORY_MB, redirect stderr to memory_statement.log
in the job directory.
Also, use -1 as the default for the final test to see if
$GALAXY_MEMORY_MB is a positive integer. This allows an admin to
differentiate between a legit case where we don't set $GALAXY_MEMORY_MB
(currently any DRM other than Slurm) and where the command ran but
returned nothing on stdout.
Commit: a18835b5169cbc281daa7de9dbfd655ab96f17f4
https://github.com/galaxyproject/galaxy/commit/a18835b5169cbc281daa7de9dbfd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
A lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/tools/xsd/galaxy.xsd
Log Message:
-----------
Merge pull request #4958 from natefoo/memory-env-var
Create the $GALAXY_MEMORY_MB tool job environment variable
Compare: https://github.com/galaxyproject/galaxy/compare/0799e511c41d...a18835b5169c
1
0
[galaxyproject/galaxy] 79e96e: Run `hg clone` in a subprocess instead of using Me...
by GitHub 13 Nov '17
by GitHub 13 Nov '17
13 Nov '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 79e96e610dfb4dc6ce53ec39fe294ddde1600651
https://github.com/galaxyproject/galaxy/commit/79e96e610dfb4dc6ce53ec39fe29…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-11-10 (Fri, 10 Nov 2017)
Changed paths:
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Run `hg clone` in a subprocess instead of using Mercurial API
Using the API is discouraged by upstream, see:
https://www.mercurial-scm.org/wiki/MercurialApi
Moreover, the old code randomly causes the following error when installing
big ToolShed repositories (e.g. any qiime tool) through the admin UI:
tool_shed.util.hg_util DEBUG 2017-11-03 17:36:45,950 Error cloning repository: signal only works in main thread
This error occurs when Galaxy runs under Paste and also when it runs under
uWSGI with multiple threads per process.
Commit: 0799e511c41d8a739dc5e137e70848c079da92ea
https://github.com/galaxyproject/galaxy/commit/0799e511c41d8a739dc5e137e708…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/tool_shed/util/hg_util.py
Log Message:
-----------
Merge pull request #4979 from nsoranzo/hg_clone
Run `hg clone` in a subprocess instead of using Mercurial API
Compare: https://github.com/galaxyproject/galaxy/compare/87ebf9c54ae6...0799e511c41d
1
0
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: 231ce40e8154bd44fc1e5a0072489b9b81ad5377
https://github.com/galaxyproject/galaxy/commit/231ce40e8154bd44fc1e5a007248…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-12 (Sun, 12 Nov 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Encode file content with utf-8
There shouldn't be any disadvantages over doing this only for specific elements.
This also fixes https://github.com/galaxyproject/galaxy/issues/4345#issuecomment-343753378.
I have tested this with unicode strings in the name and info fields.
Commit: 0c9b42035bc51d6a66f5a6e0746fd28c67996cb3
https://github.com/galaxyproject/galaxy/commit/0c9b42035bc51d6a66f5a6e0746f…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Open files in text-mode (thx @nsoranzo)
Commit: a0b4a2de53793c85a9b0443be4b2e4a8f4421759
https://github.com/galaxyproject/galaxy/commit/a0b4a2de53793c85a9b0443be4b2…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/imp_exp/__init__.py
Log Message:
-----------
Merge pull request #4987 from mvdbeek/history_import_bug
[17.09][Bug] Encode file content with utf-8
Compare: https://github.com/galaxyproject/galaxy/compare/222ece4eabb6...a0b4a2de5379
1
0
[galaxyproject/galaxy] 6d5b7c: Install numpy before bx-python in case you are ins...
by GitHub 13 Nov '17
by GitHub 13 Nov '17
13 Nov '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 6d5b7c0ebc588c12f55ada87b2b900b66e8c8114
https://github.com/galaxyproject/galaxy/commit/6d5b7c0ebc588c12f55ada87b2b9…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-11 (Sat, 11 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Install numpy before bx-python in case you are installing from sdists.
Commit: 8079dd5fc03bb034e99bdf995eaf6f1e7bc32050
https://github.com/galaxyproject/galaxy/commit/8079dd5fc03bb034e99bdf995eaf…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Add comment about numpy order in requirements.
As requested by @nsoranzo.
Commit: 87ebf9c54ae62948dfa22b8c8bc8b7ca3b5e31d1
https://github.com/galaxyproject/galaxy/commit/87ebf9c54ae62948dfa22b8c8bc8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Merge pull request #4982 from natefoo/source-requirements
Install numpy before bx-python in case you are installing from sdists
Compare: https://github.com/galaxyproject/galaxy/compare/a2c164a53ad9...87ebf9c54ae6
1
0
13 Nov '17
Branch: refs/heads/release_17.05
Home: https://github.com/galaxyproject/galaxy
Commit: b6a0a1b084fe09de394aa6d0fb3caabc9fdf98a3
https://github.com/galaxyproject/galaxy/commit/b6a0a1b084fe09de394aa6d0fb3c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-11 (Sat, 11 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Tolerate IOError in tool and data table watcher
Without these changes the watcher thread may die when manually deleting loc files:
```
Exception in thread Thread-7:
Traceback (most recent call last):
File "/usr/local/Cellar/python/2.7.13_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/threading.py", line 801, in __bootstrap_inner
self.run()
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 199, in run
self.dispatch_events(self.event_queue, self.timeout)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/observers/api.py", line 368, in dispatch_events
handler.dispatch(event)
File "/Users/mvandenb/src/galaxy/.venv/lib/python2.7/site-packages/watchdog/events.py", line 322, in dispatch
self.on_any_event(event)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 226, in on_any_event
self._handle(event)
File "/Users/mvandenb/src/galaxy/lib/galaxy/tools/toolbox/watcher.py", line 235, in _handle
cur_hash = md5_hash_file(path)
File "/Users/mvandenb/src/galaxy/lib/galaxy/util/hash_util.py", line 23, in md5_hash_file
with open(path, 'rb') as afile:
IOError: [Errno 2] No such file or directory: '/Users/mvandenb/src/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/620d5603d1a8/sam_fa_indices.loc'
```
Similar problems could occur when deleting tool xml files.
Commit: 6915007f85482648999768eecb9920da57b42e59
https://github.com/galaxyproject/galaxy/commit/6915007f85482648999768eecb99…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/cache.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/util/hash_util.py
Log Message:
-----------
Merge pull request #4981 from mvdbeek/watcher_error_delete
[17.05][BUG] Tolerate IOError in tool and data table watcher
Compare: https://github.com/galaxyproject/galaxy/compare/7688b057e604...6915007f8548
1
0
[galaxyproject/galaxy] 84c925: Bumping pysam to 0.12 *core*, without customizatio...
by GitHub 13 Nov '17
by GitHub 13 Nov '17
13 Nov '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 84c92590635358a0c0798dfc8aa8ae6d2b37660e
https://github.com/galaxyproject/galaxy/commit/84c92590635358a0c0798dfc8aa8…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/visualization/data_providers/genome.py
Log Message:
-----------
Bumping pysam to 0.12 *core*, without customization
Commit: dadb3680f59e4646a53589d572d25df06d3850ed
https://github.com/galaxyproject/galaxy/commit/dadb3680f59e4646a53589d572d2…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-09-08 (Fri, 08 Sep 2017)
Changed paths:
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
Log Message:
-----------
Separate non-stdlib pysam from other imports.
Commit: ee120745afa1e30a58287591fa9fe5776c83abfa
https://github.com/galaxyproject/galaxy/commit/ee120745afa1e30a58287591fa9f…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M lib/galaxy/dependencies/pinned-requirements.txt
Log Message:
-----------
Explicitly pin pysam to 0.12.0.1
Commit: c04cf6b228ec44ae1ec97820947954551cc1a33a
https://github.com/galaxyproject/galaxy/commit/c04cf6b228ec44ae1ec978209479…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-11 (Mon, 11 Sep 2017)
Changed paths:
M scripts/common_startup.sh
Log Message:
-----------
Explicitly include PyPI as an --extra-index-url to pip so we can install
from PyPI even when a package exists (but the correct version or
architecture does not exist) on wheels.galaxyproject.org. Previously,
PyPI was only checked after wheels.galaxyproject.org because pypiserver
performs an automatic redirect to PyPI for any packages that do not
exist in its index.
Commit: 74665db45d10508030db8457529af4830a51caff
https://github.com/galaxyproject/galaxy/commit/74665db45d10508030db8457529a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-06 (Mon, 06 Nov 2017)
Changed paths:
M .ci/flake8_lint_include_list.txt
R .ci/flake8_py3_wrapper.sh
A .ci/jenkins/selenium-compose/Dockerfile
A .ci/jenkins/selenium-compose/docker-compose.yml
A .ci/jenkins/selenium-compose/galaxy.ini
A .ci/jenkins/selenium-compose/run_galaxy.bash
A .ci/jenkins/selenium-compose/run_tests.sh
R .ci/jenkins/selenium/Dockerfile
R .ci/jenkins/selenium/docker-compose.yml
R .ci/jenkins/selenium/galaxy.ini
R .ci/jenkins/selenium/run_galaxy.bash
M .ci/jenkins/selenium/run_tests.sh
M .ci/py3_sources.txt
M .gitignore
M .travis.yml
M CITATION
M Makefile
A client/.babelrc
M client/GruntFile.js
M client/README.md
M client/bower.json
M client/galaxy/scripts/admin.toolshed.js
M client/galaxy/scripts/apps/admin.js
M client/galaxy/scripts/apps/analysis.js
M client/galaxy/scripts/apps/login.js
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/apps/panels/history-panel.js
M client/galaxy/scripts/apps/panels/tool-panel.js
M client/galaxy/scripts/galaxy.interactive_environments.js
M client/galaxy/scripts/galaxy.js
M client/galaxy/scripts/galaxy.library.js
M client/galaxy/scripts/galaxy.pages.js
M client/galaxy/scripts/i18n.js
M client/galaxy/scripts/layout/generic-nav-view.js
M client/galaxy/scripts/layout/masthead.js
M client/galaxy/scripts/layout/menu.js
M client/galaxy/scripts/layout/modal.js
M client/galaxy/scripts/layout/page.js
M client/galaxy/scripts/layout/panel.js
M client/galaxy/scripts/layout/router.js
M client/galaxy/scripts/layout/scratchbook.js
R client/galaxy/scripts/libs/backbone.js
R client/galaxy/scripts/libs/bibtex.js
R client/galaxy/scripts/libs/d3.js
R client/galaxy/scripts/libs/jquery.complexify.js
R client/galaxy/scripts/libs/jquery/jquery.cookie.js
R client/galaxy/scripts/libs/jquery/jquery.js
R client/galaxy/scripts/libs/jquery/jquery.migrate.js
R client/galaxy/scripts/libs/jquery/jquery.mousewheel.js
R client/galaxy/scripts/libs/raven.js
R client/galaxy/scripts/libs/require.js
R client/galaxy/scripts/libs/underscore.js
M client/galaxy/scripts/mvc/annotation.js
M client/galaxy/scripts/mvc/base-mvc.js
M client/galaxy/scripts/mvc/base/controlled-fetch-collection.js
M client/galaxy/scripts/mvc/citation/citation-model.js
M client/galaxy/scripts/mvc/citation/citation-view.js
M client/galaxy/scripts/mvc/collection/base-creator.js
M client/galaxy/scripts/mvc/collection/collection-li-edit.js
M client/galaxy/scripts/mvc/collection/collection-li.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view-edit.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/collection/list-collection-creator.js
M client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js
M client/galaxy/scripts/mvc/collection/pair-collection-creator.js
M client/galaxy/scripts/mvc/dataset/data.js
M client/galaxy/scripts/mvc/dataset/dataset-choice.js
M client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
M client/galaxy/scripts/mvc/dataset/dataset-error.js
M client/galaxy/scripts/mvc/dataset/dataset-li-edit.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/dataset/dataset-list.js
M client/galaxy/scripts/mvc/dataset/dataset-model.js
M client/galaxy/scripts/mvc/dataset/states.js
M client/galaxy/scripts/mvc/form/form-data.js
M client/galaxy/scripts/mvc/form/form-input.js
M client/galaxy/scripts/mvc/form/form-parameters.js
M client/galaxy/scripts/mvc/form/form-repeat.js
M client/galaxy/scripts/mvc/form/form-section.js
M client/galaxy/scripts/mvc/form/form-view.js
M client/galaxy/scripts/mvc/form/form-wrapper.js
M client/galaxy/scripts/mvc/grid/grid-model.js
M client/galaxy/scripts/mvc/grid/grid-shared.js
M client/galaxy/scripts/mvc/grid/grid-template.js
M client/galaxy/scripts/mvc/grid/grid-view.js
M client/galaxy/scripts/mvc/history/copy-dialog.js
M client/galaxy/scripts/mvc/history/hda-li-edit.js
M client/galaxy/scripts/mvc/history/hda-li.js
M client/galaxy/scripts/mvc/history/hda-model.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/scripts/mvc/history/hdca-li.js
M client/galaxy/scripts/mvc/history/hdca-model.js
M client/galaxy/scripts/mvc/history/history-content-model.js
M client/galaxy/scripts/mvc/history/history-contents.js
M client/galaxy/scripts/mvc/history/history-list.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-preferences.js
M client/galaxy/scripts/mvc/history/history-structure-view.js
M client/galaxy/scripts/mvc/history/history-view-annotated.js
M client/galaxy/scripts/mvc/history/history-view-edit-current.js
M client/galaxy/scripts/mvc/history/history-view-edit.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/history/job-dag.js
M client/galaxy/scripts/mvc/history/multi-panel.js
M client/galaxy/scripts/mvc/history/options-menu.js
M client/galaxy/scripts/mvc/job/job-li.js
M client/galaxy/scripts/mvc/job/job-model.js
M client/galaxy/scripts/mvc/job/job-params.js
A client/galaxy/scripts/mvc/lazy/lazy-limited.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-folderlist-view.js
M client/galaxy/scripts/mvc/library/library-folderrow-view.js
M client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
M client/galaxy/scripts/mvc/library/library-library-view.js
M client/galaxy/scripts/mvc/library/library-librarylist-view.js
M client/galaxy/scripts/mvc/library/library-libraryrow-view.js
M client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
M client/galaxy/scripts/mvc/library/library-model.js
A client/galaxy/scripts/mvc/library/library-util.js
M client/galaxy/scripts/mvc/list/list-item.js
M client/galaxy/scripts/mvc/list/list-view.js
M client/galaxy/scripts/mvc/tag.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/tool/tool-genomespace.js
M client/galaxy/scripts/mvc/tool/tools.js
M client/galaxy/scripts/mvc/toolshed/categories-view.js
M client/galaxy/scripts/mvc/toolshed/repo-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repo-status-view.js
M client/galaxy/scripts/mvc/toolshed/repositories-view.js
M client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
M client/galaxy/scripts/mvc/toolshed/repository-view.js
M client/galaxy/scripts/mvc/toolshed/shed-list-view.js
M client/galaxy/scripts/mvc/toolshed/toolshed-model.js
M client/galaxy/scripts/mvc/toolshed/util.js
M client/galaxy/scripts/mvc/toolshed/workflows-view.js
M client/galaxy/scripts/mvc/tours.js
M client/galaxy/scripts/mvc/ui/error-modal.js
M client/galaxy/scripts/mvc/ui/icon-button.js
M client/galaxy/scripts/mvc/ui/popup-menu.js
M client/galaxy/scripts/mvc/ui/ui-buttons.js
M client/galaxy/scripts/mvc/ui/ui-color-picker.js
M client/galaxy/scripts/mvc/ui/ui-drilldown.js
M client/galaxy/scripts/mvc/ui/ui-frames.js
M client/galaxy/scripts/mvc/ui/ui-list.js
M client/galaxy/scripts/mvc/ui/ui-misc.js
M client/galaxy/scripts/mvc/ui/ui-modal.js
M client/galaxy/scripts/mvc/ui/ui-options.js
M client/galaxy/scripts/mvc/ui/ui-popover.js
M client/galaxy/scripts/mvc/ui/ui-portlet.js
M client/galaxy/scripts/mvc/ui/ui-select-content.js
M client/galaxy/scripts/mvc/ui/ui-select-default.js
M client/galaxy/scripts/mvc/ui/ui-select-ftp.js
M client/galaxy/scripts/mvc/ui/ui-select-genomespace.js
M client/galaxy/scripts/mvc/ui/ui-select-library.js
M client/galaxy/scripts/mvc/ui/ui-select.js
M client/galaxy/scripts/mvc/ui/ui-slider.js
M client/galaxy/scripts/mvc/ui/ui-table.js
M client/galaxy/scripts/mvc/ui/ui-tabs.js
M client/galaxy/scripts/mvc/ui/ui-thumbnails.js
M client/galaxy/scripts/mvc/upload/collection/collection-row.js
M client/galaxy/scripts/mvc/upload/collection/collection-view.js
M client/galaxy/scripts/mvc/upload/composite/composite-row.js
M client/galaxy/scripts/mvc/upload/composite/composite-view.js
M client/galaxy/scripts/mvc/upload/default/default-row.js
M client/galaxy/scripts/mvc/upload/default/default-view.js
M client/galaxy/scripts/mvc/upload/upload-button.js
A client/galaxy/scripts/mvc/upload/upload-extension.js
M client/galaxy/scripts/mvc/upload/upload-ftp.js
M client/galaxy/scripts/mvc/upload/upload-model.js
M client/galaxy/scripts/mvc/upload/upload-settings.js
M client/galaxy/scripts/mvc/upload/upload-view.js
M client/galaxy/scripts/mvc/user/user-custom-builds.js
M client/galaxy/scripts/mvc/user/user-model.js
M client/galaxy/scripts/mvc/user/user-preferences.js
M client/galaxy/scripts/mvc/user/user-quotameter.js
M client/galaxy/scripts/mvc/visualization/visualization-model.js
M client/galaxy/scripts/mvc/webhooks.js
M client/galaxy/scripts/mvc/workflow/workflow-canvas.js
M client/galaxy/scripts/mvc/workflow/workflow-connector.js
M client/galaxy/scripts/mvc/workflow/workflow-forms.js
M client/galaxy/scripts/mvc/workflow/workflow-icons.js
M client/galaxy/scripts/mvc/workflow/workflow-manager.js
M client/galaxy/scripts/mvc/workflow/workflow-model.js
M client/galaxy/scripts/mvc/workflow/workflow-node.js
M client/galaxy/scripts/mvc/workflow/workflow-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view-data.js
M client/galaxy/scripts/mvc/workflow/workflow-view-node.js
M client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js
M client/galaxy/scripts/mvc/workflow/workflow-view.js
M client/galaxy/scripts/mvc/workflow/workflow.js
M client/galaxy/scripts/nls/de/locale.js
M client/galaxy/scripts/nls/es/locale.js
M client/galaxy/scripts/nls/fr/locale.js
M client/galaxy/scripts/nls/ja/locale.js
M client/galaxy/scripts/nls/locale.js
M client/galaxy/scripts/nls/zh/locale.js
M client/galaxy/scripts/onload.js
M client/galaxy/scripts/polyfills.js
M client/galaxy/scripts/reports_webapp/run_stats.js
M client/galaxy/scripts/ui/autocom_tagging.js
M client/galaxy/scripts/ui/editable-text.js
M client/galaxy/scripts/ui/fa-icon-button.js
M client/galaxy/scripts/ui/filter-control.js
M client/galaxy/scripts/ui/hoverhighlight.js
M client/galaxy/scripts/ui/loading-indicator.js
M client/galaxy/scripts/ui/mode-button.js
M client/galaxy/scripts/ui/pagination.js
M client/galaxy/scripts/ui/peek-column-selector.js
M client/galaxy/scripts/ui/popupmenu.js
M client/galaxy/scripts/ui/scroll-panel.js
M client/galaxy/scripts/ui/search-input.js
M client/galaxy/scripts/utils/add-logging.js
M client/galaxy/scripts/utils/ajax-queue.js
M client/galaxy/scripts/utils/async-save-text.js
M client/galaxy/scripts/utils/config.js
M client/galaxy/scripts/utils/deferred.js
M client/galaxy/scripts/utils/graph.js
M client/galaxy/scripts/utils/levenshtein.js
M client/galaxy/scripts/utils/localization.js
M client/galaxy/scripts/utils/metrics-logger.js
M client/galaxy/scripts/utils/natural-sort.js
M client/galaxy/scripts/utils/query-string-parsing.js
M client/galaxy/scripts/utils/uploadbox.js
M client/galaxy/scripts/utils/utils.js
M client/galaxy/scripts/viz/bbi-data-manager.js
M client/galaxy/scripts/viz/circster.js
M client/galaxy/scripts/viz/phyloviz.js
M client/galaxy/scripts/viz/sweepster.js
M client/galaxy/scripts/viz/trackster.js
M client/galaxy/scripts/viz/trackster/filters.js
M client/galaxy/scripts/viz/trackster/painters.js
M client/galaxy/scripts/viz/trackster/slotting.js
M client/galaxy/scripts/viz/trackster/tracks.js
M client/galaxy/scripts/viz/trackster/util.js
M client/galaxy/scripts/viz/visualization.js
M client/galaxy/scripts/viz/viz_views.js
M client/galaxy/style/less/base.less
M client/galaxy/style/less/library.less
M client/galaxy/style/less/ui.less
M client/galaxy/style/less/upload.less
M client/grunt-tasks/install-libs.js
M client/grunt-tasks/style.js
R client/grunt-tasks/webpack.js
A client/gulpfile.js
R client/package-lock.json
M client/package.json
M client/toolshed/scripts/mvc/groups/group-detail-view.js
M client/toolshed/scripts/mvc/groups/group-list-view.js
M client/toolshed/scripts/mvc/groups/group-model.js
M client/webpack.config.js
A client/yarn.lock
M config/datatypes_conf.xml.sample
M config/error_report.yml.sample
M config/galaxy.ini.sample
M config/local_conda_mapping.yml.sample
M config/plugins/interactive_environments/bam_iobio/static/js/bam_iobio.js
M config/plugins/interactive_environments/bam_iobio/templates/bam_iobio.mako
M config/plugins/interactive_environments/common/templates/ie.mako
M config/plugins/interactive_environments/ethercalc/static/js/ethercalc.js
M config/plugins/interactive_environments/ethercalc/templates/ethercalc.mako
M config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
M config/plugins/interactive_environments/hicbrowser/templates/hicbrowser.mako
M config/plugins/interactive_environments/jupyter/static/js/jupyter.js
M config/plugins/interactive_environments/jupyter/templates/jupyter.mako
M config/plugins/interactive_environments/neo/static/js/neo.js
M config/plugins/interactive_environments/neo/templates/neo.mako
M config/plugins/interactive_environments/phinch/static/js/phinch.js
M config/plugins/interactive_environments/phinch/templates/phinch.mako
M config/plugins/interactive_environments/rstudio/static/js/rstudio.js
M config/plugins/interactive_environments/rstudio/templates/rstudio.mako
M config/plugins/tours/core.galaxy_ui.yaml
M config/plugins/tours/core.history.yaml
M config/plugins/tours/core.scratchbook.yaml
M config/plugins/visualizations/charts/static/repository/build/registry.js
M config/plugins/visualizations/charts/static/repository/build/registry.js.map
M config/plugins/visualizations/charts/webpack.config.js
M config/plugins/webhooks/demo/tour_generator/helper/__init__.py
M config/plugins/webhooks/demo/tour_generator/static/script.js
M contrib/galaxy_config_merger.py
M create_db.sh
M cron/add_manual_builds.py
M cron/build_chrom_db.py
M cron/parse_builds.py
M cron/parse_builds_3_sites.py
M doc/schema_template.md
M doc/source/admin/reports.md
M doc/source/project/issues.rst
A doc/source/releases/17.09.rst
M doc/source/releases/17.09_announce.rst
A doc/source/releases/18.01_announce.rst
M doc/source/releases/index.rst
M doc/source/slideshow/architecture/galaxy_architecture.md
M extract_dataset_parts.sh
M lib/galaxy/__init__.py
M lib/galaxy/app.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/config.py
M lib/galaxy/containers/__init__.py
M lib/galaxy/containers/docker_model.py
M lib/galaxy/dataset_collections/type_description.py
A lib/galaxy/datatypes/annotation.py
M lib/galaxy/datatypes/assembly.py
M lib/galaxy/datatypes/binary.py
M lib/galaxy/datatypes/constructive_solid_geometry.py
R lib/galaxy/datatypes/converters/bam_to_bai.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
M lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
M lib/galaxy/datatypes/converters/gff_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bed_converter.py
M lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
M lib/galaxy/datatypes/converters/interval_to_coverage.py
M lib/galaxy/datatypes/converters/interval_to_fli.py
M lib/galaxy/datatypes/converters/lped_to_fped_converter.py
M lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
M lib/galaxy/datatypes/converters/maf_to_fasta_converter.py
M lib/galaxy/datatypes/converters/maf_to_interval_converter.py
M lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
M lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
M lib/galaxy/datatypes/converters/picard_interval_list_to_bed6_converter.py
M lib/galaxy/datatypes/converters/sam_to_bam.py
M lib/galaxy/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/base.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/dataproviders/external.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/genetics.py
M lib/galaxy/datatypes/images.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/molecules.py
M lib/galaxy/datatypes/mothur.py
M lib/galaxy/datatypes/msa.py
M lib/galaxy/datatypes/ngsindex.py
M lib/galaxy/datatypes/plant_tribes.py
M lib/galaxy/datatypes/proteomics.py
M lib/galaxy/datatypes/qualityscore.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/chebi_57262.v3k.mol
A lib/galaxy/datatypes/test/github88.v3k.sdf
A lib/galaxy/datatypes/test/mothur_datatypetest_false_2.mothur.freq
A lib/galaxy/datatypes/test/postgresql_fake.tar.bz2
A lib/galaxy/datatypes/test/test.fast5.tar
A lib/galaxy/datatypes/test/test.fast5.tar.bz2
A lib/galaxy/datatypes/test/test.fast5.tar.gz
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M lib/galaxy/jobs/output_checker.py
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M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
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M static/maps/mvc/grid/grid-template.js.map
M static/maps/mvc/grid/grid-view.js.map
M static/maps/mvc/history/copy-dialog.js.map
M static/maps/mvc/history/hda-li-edit.js.map
M static/maps/mvc/history/hda-li.js.map
M static/maps/mvc/history/hda-model.js.map
M static/maps/mvc/history/hdca-li-edit.js.map
M static/maps/mvc/history/hdca-li.js.map
M static/maps/mvc/history/hdca-model.js.map
M static/maps/mvc/history/history-content-model.js.map
M static/maps/mvc/history/history-contents.js.map
M static/maps/mvc/history/history-list.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-preferences.js.map
M static/maps/mvc/history/history-structure-view.js.map
M static/maps/mvc/history/history-view-annotated.js.map
M static/maps/mvc/history/history-view-edit-current.js.map
M static/maps/mvc/history/history-view-edit.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/history/job-dag.js.map
M static/maps/mvc/history/multi-panel.js.map
M static/maps/mvc/history/options-menu.js.map
M static/maps/mvc/job/job-li.js.map
M static/maps/mvc/job/job-model.js.map
M static/maps/mvc/job/job-params.js.map
A static/maps/mvc/lazy/lazy-limited.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-folderlist-view.js.map
M static/maps/mvc/library/library-folderrow-view.js.map
M static/maps/mvc/library/library-foldertoolbar-view.js.map
M static/maps/mvc/library/library-library-view.js.map
M static/maps/mvc/library/library-librarylist-view.js.map
M static/maps/mvc/library/library-libraryrow-view.js.map
M static/maps/mvc/library/library-librarytoolbar-view.js.map
M static/maps/mvc/library/library-model.js.map
A static/maps/mvc/library/library-util.js.map
M static/maps/mvc/list/list-item.js.map
M static/maps/mvc/list/list-view.js.map
A static/maps/mvc/page/page-list.js.map
M static/maps/mvc/tag.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/mvc/tool/tool-form-composite.js.map
M static/maps/mvc/tool/tool-form.js.map
M static/maps/mvc/tool/tool-genomespace.js.map
M static/maps/mvc/tool/tools.js.map
M static/maps/mvc/toolshed/categories-view.js.map
M static/maps/mvc/toolshed/repo-queue-view.js.map
M static/maps/mvc/toolshed/repo-status-view.js.map
M static/maps/mvc/toolshed/repositories-view.js.map
M static/maps/mvc/toolshed/repository-queue-view.js.map
M static/maps/mvc/toolshed/repository-view.js.map
M static/maps/mvc/toolshed/shed-list-view.js.map
M static/maps/mvc/toolshed/toolshed-model.js.map
M static/maps/mvc/toolshed/util.js.map
M static/maps/mvc/toolshed/workflows-view.js.map
M static/maps/mvc/tours.js.map
M static/maps/mvc/ui/error-modal.js.map
M static/maps/mvc/ui/icon-button.js.map
M static/maps/mvc/ui/popup-menu.js.map
M static/maps/mvc/ui/ui-buttons.js.map
M static/maps/mvc/ui/ui-color-picker.js.map
M static/maps/mvc/ui/ui-drilldown.js.map
M static/maps/mvc/ui/ui-frames.js.map
M static/maps/mvc/ui/ui-list.js.map
M static/maps/mvc/ui/ui-misc.js.map
M static/maps/mvc/ui/ui-modal.js.map
M static/maps/mvc/ui/ui-options.js.map
M static/maps/mvc/ui/ui-popover.js.map
M static/maps/mvc/ui/ui-portlet.js.map
M static/maps/mvc/ui/ui-select-content.js.map
M static/maps/mvc/ui/ui-select-default.js.map
M static/maps/mvc/ui/ui-select-ftp.js.map
M static/maps/mvc/ui/ui-select-genomespace.js.map
M static/maps/mvc/ui/ui-select-library.js.map
M static/maps/mvc/ui/ui-select.js.map
M static/maps/mvc/ui/ui-slider.js.map
M static/maps/mvc/ui/ui-table.js.map
M static/maps/mvc/ui/ui-tabs.js.map
M static/maps/mvc/ui/ui-thumbnails.js.map
M static/maps/mvc/upload/collection/collection-row.js.map
M static/maps/mvc/upload/collection/collection-view.js.map
M static/maps/mvc/upload/composite/composite-row.js.map
M static/maps/mvc/upload/composite/composite-view.js.map
M static/maps/mvc/upload/default/default-row.js.map
M static/maps/mvc/upload/default/default-view.js.map
M static/maps/mvc/upload/upload-button.js.map
A static/maps/mvc/upload/upload-extension.js.map
M static/maps/mvc/upload/upload-ftp.js.map
M static/maps/mvc/upload/upload-model.js.map
M static/maps/mvc/upload/upload-settings.js.map
M static/maps/mvc/upload/upload-view.js.map
M static/maps/mvc/user/user-custom-builds.js.map
M static/maps/mvc/user/user-model.js.map
M static/maps/mvc/user/user-preferences.js.map
M static/maps/mvc/user/user-quotameter.js.map
M static/maps/mvc/visualization/visualization-model.js.map
M static/maps/mvc/webhooks.js.map
M static/maps/mvc/workflow/workflow-canvas.js.map
M static/maps/mvc/workflow/workflow-configure-menu.js.map
M static/maps/mvc/workflow/workflow-connector.js.map
M static/maps/mvc/workflow/workflow-forms.js.map
M static/maps/mvc/workflow/workflow-icons.js.map
M static/maps/mvc/workflow/workflow-manager.js.map
M static/maps/mvc/workflow/workflow-model.js.map
M static/maps/mvc/workflow/workflow-node.js.map
M static/maps/mvc/workflow/workflow-terminals.js.map
M static/maps/mvc/workflow/workflow-view-data.js.map
M static/maps/mvc/workflow/workflow-view-node.js.map
M static/maps/mvc/workflow/workflow-view-terminals.js.map
M static/maps/mvc/workflow/workflow-view.js.map
M static/maps/mvc/workflow/workflow.js.map
M static/maps/nls/de/locale.js.map
M static/maps/nls/es/locale.js.map
M static/maps/nls/fr/locale.js.map
M static/maps/nls/ja/locale.js.map
M static/maps/nls/locale.js.map
M static/maps/nls/zh/locale.js.map
M static/maps/onload.js.map
M static/maps/polyfills.js.map
M static/maps/reports_webapp/run_stats.js.map
M static/maps/ui/autocom_tagging.js.map
M static/maps/ui/editable-text.js.map
M static/maps/ui/fa-icon-button.js.map
M static/maps/ui/filter-control.js.map
M static/maps/ui/hoverhighlight.js.map
M static/maps/ui/loading-indicator.js.map
M static/maps/ui/mode-button.js.map
M static/maps/ui/pagination.js.map
M static/maps/ui/peek-column-selector.js.map
M static/maps/ui/popupmenu.js.map
M static/maps/ui/scroll-panel.js.map
M static/maps/ui/search-input.js.map
M static/maps/utils/add-logging.js.map
M static/maps/utils/ajax-queue.js.map
M static/maps/utils/async-save-text.js.map
M static/maps/utils/config.js.map
M static/maps/utils/deferred.js.map
M static/maps/utils/graph.js.map
M static/maps/utils/levenshtein.js.map
M static/maps/utils/localization.js.map
M static/maps/utils/metrics-logger.js.map
M static/maps/utils/natural-sort.js.map
M static/maps/utils/query-string-parsing.js.map
M static/maps/utils/uploadbox.js.map
M static/maps/utils/utils.js.map
M static/maps/viz/bbi-data-manager.js.map
M static/maps/viz/circster.js.map
M static/maps/viz/phyloviz.js.map
M static/maps/viz/sweepster.js.map
M static/maps/viz/trackster.js.map
M static/maps/viz/trackster/filters.js.map
M static/maps/viz/trackster/painters.js.map
M static/maps/viz/trackster/slotting.js.map
M static/maps/viz/trackster/tracks.js.map
M static/maps/viz/trackster/util.js.map
M static/maps/viz/visualization.js.map
M static/maps/viz/viz_views.js.map
M static/scripts/admin.toolshed.js
R static/scripts/analysis.js
R static/scripts/app.js
R static/scripts/app/analysis.js
M static/scripts/bundled/admin.bundled.js
M static/scripts/bundled/admin.bundled.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/bundled/login.bundled.js
M static/scripts/bundled/login.bundled.js.map
M static/scripts/galaxy.interactive_environments.js
M static/scripts/galaxy.js
M static/scripts/galaxy.library.js
R static/scripts/galaxy.menu.js
M static/scripts/galaxy.pages.js
M static/scripts/i18n.js
M static/scripts/layout/generic-nav-view.js
M static/scripts/layout/masthead.js
M static/scripts/layout/menu.js
M static/scripts/layout/modal.js
M static/scripts/layout/page.js
M static/scripts/layout/panel.js
M static/scripts/layout/router.js
M static/scripts/layout/scratchbook.js
M static/scripts/libs/backbone.js
M static/scripts/libs/bbi/bigwig.js
M static/scripts/libs/bbi/jquery-ajax-native.js
M static/scripts/libs/bbi/jszlib.js
M static/scripts/libs/bbi/spans.js
M static/scripts/libs/bibtex.js
M static/scripts/libs/bootstrap-tour.js
M static/scripts/libs/bootstrap.js
R static/scripts/libs/common-libs.js
M static/scripts/libs/d3.js
M static/scripts/libs/farbtastic.js
R static/scripts/libs/jquery.complexify.js
M static/scripts/libs/jquery.sparklines.js
R static/scripts/libs/jquery/jqtouch.js
M static/scripts/libs/jquery/jquery-ui.js
M static/scripts/libs/jquery/jquery.autocomplete.js
A static/scripts/libs/jquery/jquery.complexify.js
M static/scripts/libs/jquery/jquery.cookie.js
M static/scripts/libs/jquery/jquery.dynatree.js
M static/scripts/libs/jquery/jquery.event.drag.js
M static/scripts/libs/jquery/jquery.event.drop.js
M static/scripts/libs/jquery/jquery.event.hover.js
M static/scripts/libs/jquery/jquery.form.js
M static/scripts/libs/jquery/jquery.js
M static/scripts/libs/jquery/jquery.migrate.js
M static/scripts/libs/jquery/jquery.mousewheel.js
M static/scripts/libs/jquery/jquery.rating.js
M static/scripts/libs/jquery/jquery.wymeditor.js
M static/scripts/libs/jquery/jstorage.js
M static/scripts/libs/jquery/jstree.js
M static/scripts/libs/jquery/select2.js
M static/scripts/libs/raven.js
M static/scripts/libs/require.js
R static/scripts/libs/showdown.js
M static/scripts/libs/toastr.js
M static/scripts/libs/underscore.js
M static/scripts/mvc/annotation.js
M static/scripts/mvc/base-mvc.js
M static/scripts/mvc/base/controlled-fetch-collection.js
M static/scripts/mvc/citation/citation-model.js
M static/scripts/mvc/citation/citation-view.js
M static/scripts/mvc/collection/base-creator.js
M static/scripts/mvc/collection/collection-li-edit.js
M static/scripts/mvc/collection/collection-li.js
M static/scripts/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view-edit.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/collection/list-collection-creator.js
M static/scripts/mvc/collection/list-of-pairs-collection-creator.js
M static/scripts/mvc/collection/pair-collection-creator.js
M static/scripts/mvc/dataset/data.js
M static/scripts/mvc/dataset/dataset-choice.js
M static/scripts/mvc/dataset/dataset-edit-attributes.js
M static/scripts/mvc/dataset/dataset-error.js
M static/scripts/mvc/dataset/dataset-li-edit.js
M static/scripts/mvc/dataset/dataset-li.js
M static/scripts/mvc/dataset/dataset-list.js
M static/scripts/mvc/dataset/dataset-model.js
M static/scripts/mvc/dataset/states.js
M static/scripts/mvc/form/form-data.js
M static/scripts/mvc/form/form-input.js
M static/scripts/mvc/form/form-parameters.js
M static/scripts/mvc/form/form-repeat.js
M static/scripts/mvc/form/form-section.js
M static/scripts/mvc/form/form-view.js
M static/scripts/mvc/form/form-wrapper.js
M static/scripts/mvc/grid/grid-model.js
M static/scripts/mvc/grid/grid-shared.js
M static/scripts/mvc/grid/grid-template.js
M static/scripts/mvc/grid/grid-view.js
M static/scripts/mvc/history/copy-dialog.js
M static/scripts/mvc/history/hda-li-edit.js
M static/scripts/mvc/history/hda-li.js
M static/scripts/mvc/history/hda-model.js
M static/scripts/mvc/history/hdca-li-edit.js
M static/scripts/mvc/history/hdca-li.js
M static/scripts/mvc/history/hdca-model.js
M static/scripts/mvc/history/history-content-model.js
M static/scripts/mvc/history/history-contents.js
M static/scripts/mvc/history/history-list.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-preferences.js
M static/scripts/mvc/history/history-structure-view.js
M static/scripts/mvc/history/history-view-annotated.js
M static/scripts/mvc/history/history-view-edit-current.js
M static/scripts/mvc/history/history-view-edit.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/history/job-dag.js
M static/scripts/mvc/history/multi-panel.js
M static/scripts/mvc/history/options-menu.js
M static/scripts/mvc/job/job-li.js
M static/scripts/mvc/job/job-model.js
M static/scripts/mvc/job/job-params.js
A static/scripts/mvc/lazy/lazy-limited.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-folderlist-view.js
M static/scripts/mvc/library/library-folderrow-view.js
M static/scripts/mvc/library/library-foldertoolbar-view.js
M static/scripts/mvc/library/library-library-view.js
M static/scripts/mvc/library/library-librarylist-view.js
M static/scripts/mvc/library/library-libraryrow-view.js
M static/scripts/mvc/library/library-librarytoolbar-view.js
M static/scripts/mvc/library/library-model.js
A static/scripts/mvc/library/library-util.js
M static/scripts/mvc/list/list-item.js
M static/scripts/mvc/list/list-view.js
M static/scripts/mvc/tag.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/mvc/tool/tool-form-composite.js
M static/scripts/mvc/tool/tool-form.js
M static/scripts/mvc/tool/tool-genomespace.js
R static/scripts/mvc/tool/tool-template.js
R static/scripts/mvc/tool/tool-webhooks.js
M static/scripts/mvc/tool/tools.js
M static/scripts/mvc/toolshed/categories-view.js
M static/scripts/mvc/toolshed/repo-queue-view.js
M static/scripts/mvc/toolshed/repo-status-view.js
M static/scripts/mvc/toolshed/repositories-view.js
M static/scripts/mvc/toolshed/repository-queue-view.js
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R static/scripts/mvc/toolshed/shed-category-view.js
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R static/scripts/mvc/toolshed/shed-repo-details-view.js
R static/scripts/mvc/toolshed/shed-repo-list-view.js
R static/scripts/mvc/toolshed/sheds-list-view.js
M static/scripts/mvc/toolshed/toolshed-model.js
M static/scripts/mvc/toolshed/util.js
M static/scripts/mvc/toolshed/workflows-view.js
M static/scripts/mvc/tours.js
M static/scripts/mvc/ui/error-modal.js
M static/scripts/mvc/ui/icon-button.js
M static/scripts/mvc/ui/popup-menu.js
M static/scripts/mvc/ui/ui-buttons.js
M static/scripts/mvc/ui/ui-color-picker.js
M static/scripts/mvc/ui/ui-drilldown.js
M static/scripts/mvc/ui/ui-frames.js
M static/scripts/mvc/ui/ui-list.js
M static/scripts/mvc/ui/ui-misc.js
M static/scripts/mvc/ui/ui-modal.js
M static/scripts/mvc/ui/ui-options.js
M static/scripts/mvc/ui/ui-popover.js
M static/scripts/mvc/ui/ui-portlet.js
M static/scripts/mvc/ui/ui-select-content.js
M static/scripts/mvc/ui/ui-select-default.js
M static/scripts/mvc/ui/ui-select-ftp.js
M static/scripts/mvc/ui/ui-select-genomespace.js
M static/scripts/mvc/ui/ui-select-library.js
M static/scripts/mvc/ui/ui-select.js
M static/scripts/mvc/ui/ui-slider.js
M static/scripts/mvc/ui/ui-table.js
M static/scripts/mvc/ui/ui-tabs.js
M static/scripts/mvc/ui/ui-thumbnails.js
M static/scripts/mvc/upload/collection/collection-row.js
M static/scripts/mvc/upload/collection/collection-view.js
M static/scripts/mvc/upload/composite/composite-row.js
M static/scripts/mvc/upload/composite/composite-view.js
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M static/scripts/mvc/upload/default/default-view.js
M static/scripts/mvc/upload/upload-button.js
A static/scripts/mvc/upload/upload-extension.js
M static/scripts/mvc/upload/upload-ftp.js
M static/scripts/mvc/upload/upload-model.js
M static/scripts/mvc/upload/upload-settings.js
M static/scripts/mvc/upload/upload-view.js
R static/scripts/mvc/user/change-password.js
R static/scripts/mvc/user/extra-information.js
R static/scripts/mvc/user/manage-user-information.js
M static/scripts/mvc/user/user-custom-builds.js
M static/scripts/mvc/user/user-model.js
M static/scripts/mvc/user/user-preferences.js
M static/scripts/mvc/user/user-quotameter.js
M static/scripts/mvc/visualization/visualization-model.js
M static/scripts/mvc/webhooks.js
M static/scripts/mvc/workflow/workflow-canvas.js
R static/scripts/mvc/workflow/workflow-configure-menu.js
M static/scripts/mvc/workflow/workflow-connector.js
M static/scripts/mvc/workflow/workflow-forms.js
M static/scripts/mvc/workflow/workflow-icons.js
M static/scripts/mvc/workflow/workflow-manager.js
M static/scripts/mvc/workflow/workflow-model.js
M static/scripts/mvc/workflow/workflow-node.js
M static/scripts/mvc/workflow/workflow-terminals.js
M static/scripts/mvc/workflow/workflow-view-data.js
M static/scripts/mvc/workflow/workflow-view-node.js
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M static/scripts/ui/search-input.js
M static/scripts/utils/add-logging.js
M static/scripts/utils/ajax-queue.js
M static/scripts/utils/async-save-text.js
M static/scripts/utils/config.js
M static/scripts/utils/deferred.js
M static/scripts/utils/graph.js
M static/scripts/utils/levenshtein.js
M static/scripts/utils/localization.js
M static/scripts/utils/metrics-logger.js
M static/scripts/utils/natural-sort.js
M static/scripts/utils/query-string-parsing.js
M static/scripts/utils/uploadbox.js
M static/scripts/utils/utils.js
M static/scripts/viz/bbi-data-manager.js
M static/scripts/viz/circster.js
M static/scripts/viz/phyloviz.js
M static/scripts/viz/sweepster.js
M static/scripts/viz/trackster.js
M static/scripts/viz/trackster/filters.js
M static/scripts/viz/trackster/painters.js
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M static/scripts/viz/visualization.js
M static/scripts/viz/viz_views.js
M static/style/blue/base.css
M static/style/blue/library.css
M static/toolshed/maps/mvc/groups/group-detail-view.js.map
M static/toolshed/maps/mvc/groups/group-list-view.js.map
M static/toolshed/maps/mvc/groups/group-listrow-view.js.map
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R templates/admin/external_service/common.mako
R templates/admin/external_service/create_external_service.mako
R templates/admin/external_service/edit_external_service.mako
R templates/admin/external_service/grid.mako
R templates/admin/external_service/reload_external_service_types.mako
R templates/admin/external_service/view_external_service.mako
R templates/admin/forms/create_form.mako
R templates/admin/forms/edit_form_definition.mako
R templates/admin/forms/grid.mako
R templates/admin/forms/view_form_definition.mako
R templates/admin/package_tool.mako
R templates/admin/reload_tool.mako
R templates/admin/request_type/common.mako
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R templates/admin/request_type/edit_request_type.mako
R templates/admin/request_type/grid.mako
R templates/admin/request_type/request_type_permissions.mako
R templates/admin/request_type/view_request_type.mako
R templates/admin/requests/grid.mako
R templates/admin/requests/reject.mako
R templates/admin/requests/rename_datasets.mako
R templates/admin/requests/sample_datasets_grid.mako
R templates/admin/requests/view_sample_dataset.mako
R templates/admin/tool_shed_repository/browse_category.mako
R templates/admin/tool_shed_repository/initiate_repository_installation.mako
A templates/admin/tool_shed_repository/monitor_repository_installation.mako
R templates/admin/tool_shed_repository/repair_repository.mako
M templates/admin/tool_shed_repository/repository_actions_menu.mako
R templates/admin/tool_shed_repository/repository_installation_grid.mako
R templates/admin/tool_shed_repository/tool_dependencies_grid.mako
M templates/base.mako
M templates/base/base_panels.mako
M templates/display_base.mako
M templates/display_common.mako
R templates/export_base.mako
M templates/galaxy_client_app.mako
M templates/grid_base.mako
M templates/js-app.mako
R templates/rss.mako
M templates/sharing_base.mako
M templates/show_params.mako
M templates/webapps/galaxy/admin/center.mako
M templates/webapps/galaxy/admin/sanitize_whitelist.mako
R templates/webapps/galaxy/admin/toolsheds.mako
M templates/webapps/galaxy/dataset/display.mako
M templates/webapps/galaxy/dataset/tabular_chunked.mako
M templates/webapps/galaxy/galaxy.masthead.mako
M templates/webapps/galaxy/galaxy.panels.mako
M templates/webapps/galaxy/history/citations.mako
M templates/webapps/galaxy/history/display.mako
M templates/webapps/galaxy/history/display_structured.mako
M templates/webapps/galaxy/history/embed.mako
R templates/webapps/galaxy/history/permissions.mako
R templates/webapps/galaxy/history/rename.mako
M templates/webapps/galaxy/history/structure.mako
M templates/webapps/galaxy/history/view.mako
M templates/webapps/galaxy/history/view_multiple.mako
R templates/webapps/galaxy/page/create.mako
M templates/webapps/galaxy/page/editor.mako
R templates/webapps/galaxy/requests/common/add_samples.mako
R templates/webapps/galaxy/requests/common/common.mako
R templates/webapps/galaxy/requests/common/create_request.mako
R templates/webapps/galaxy/requests/common/edit_basic_request_info.mako
R templates/webapps/galaxy/requests/common/edit_samples.mako
R templates/webapps/galaxy/requests/common/find_samples.mako
R templates/webapps/galaxy/requests/common/index.mako
R templates/webapps/galaxy/requests/common/sample_dataset_transfer_status.mako
R templates/webapps/galaxy/requests/common/sample_datasets.mako
R templates/webapps/galaxy/requests/common/sample_state.mako
R templates/webapps/galaxy/requests/common/view_request.mako
R templates/webapps/galaxy/requests/common/view_request_history.mako
R templates/webapps/galaxy/requests/common/view_sample.mako
R templates/webapps/galaxy/requests/common/view_sample_datasets.mako
R templates/webapps/galaxy/requests/common/view_sample_history.mako
R templates/webapps/galaxy/requests/find_samples_index.mako
R templates/webapps/galaxy/requests/grid.mako
R templates/webapps/galaxy/requests/index.mako
R templates/webapps/galaxy/visualization/create.mako
M templates/webapps/galaxy/visualization/display.mako
M templates/webapps/galaxy/visualization/phyloviz.mako
M templates/webapps/galaxy/visualization/sweepster.mako
M templates/webapps/galaxy/workflow/editor.mako
M templates/webapps/tool_shed/group/index.mako
A test-data/selenium-test-notebook.ipynb
M test/api/test_api_batch.py
M test/api/test_authenticate.py
M test/api/test_dataset_collections.py
M test/api/test_datatypes.py
M test/api/test_histories.py
M test/api/test_history_contents.py
M test/api/test_jobs.py
M test/api/test_pages.py
M test/api/test_tools.py
A test/api/test_tools_upload.py
M test/api/test_users.py
M test/api/test_visualizations.py
M test/api/test_workflows.py
M test/api/test_workflows_from_yaml.py
M test/base/api.py
M test/base/api_util.py
A test/base/constants.py
M test/base/driver_util.py
M test/base/integration_util.py
M test/base/populators.py
M test/base/testcase.py
M test/base/workflows_format_2/converter.py
M test/base/workflows_format_2/main.py
M test/docker/base/Dockerfile
M test/docker/base/ansible_vars.yml
M test/docker/base/run_test_wrapper.sh
A test/docker/base/selenium/LICENSE
A test/docker/base/selenium/README
A test/docker/base/selenium/entry_point.sh
A test/docker/base/selenium/functions.sh
A test/docker/base/selenium/generate_config
A test/docker/base/selenium/wrap_chrome_binary
M test/functional/tools/collection_split_on_column.xml
A test/functional/tools/data_source.py
A test/functional/tools/empty_datasets.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/test_data_source.xml
M test/functional/twilltestcase.py
M test/functional/webhooks/phdcomics/helper/__init__.py
A test/galaxy_selenium/components.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/has_driver.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation-data.yml
A test/galaxy_selenium/navigation.yml
A test/galaxy_selenium/smart_components.py
A test/integration/test_data_manager_table_reload.py
M test/integration/test_resolvers.py
M test/integration/test_upload_configuration_options.py
A test/integration/tool_sheds_conf.xml
M test/manual/workflows_scaling.py
M test/qunit/Gruntfile.js
M test/qunit/package.json
M test/qunit/test-app.js
M test/qunit/test-common.js
R test/qunit/test-libs/qunit-1.23.1.css
R test/qunit/test-libs/qunit-1.23.1.js
R test/qunit/test-libs/sinon-1.17.3.js
R test/qunit/test-libs/sinon-qunit-1.0.0.js
M test/qunit/tests/form_tests.js
M test/qunit/tests/galaxy-app-base.js
M test/qunit/tests/graph.js
M test/qunit/tests/hda-base.js
M test/qunit/tests/history_contents_model_tests.js
M test/qunit/tests/job-dag.js
M test/qunit/tests/list-of-pairs-collection-creator.js
M test/qunit/tests/masthead_tests.js
M test/qunit/tests/metrics-logger.js
M test/qunit/tests/modal_tests.js
M test/qunit/tests/page_tests.js
M test/qunit/tests/popover_tests.js
M test/qunit/tests/ui_tests.js
M test/qunit/tests/upload_dialog_tests.js
M test/qunit/tests/utils_test.js
M test/qunit/tests/workflow_editor_tests.js
M test/selenium_tests/framework.py
M test/selenium_tests/test_anon_history.py
M test/selenium_tests/test_collection_builders.py
A test/selenium_tests/test_custom_builds.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_options.py
M test/selenium_tests/test_history_panel.py
M test/selenium_tests/test_history_sharing.py
A test/selenium_tests/test_jupyter.py
A test/selenium_tests/test_library_contents.py
A test/selenium_tests/test_library_landing.py
M test/selenium_tests/test_login.py
A test/selenium_tests/test_navigates_galaxy.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_registration.py
A test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_sizzle_loading.py
M test/selenium_tests/test_stock_tours.py
M test/selenium_tests/test_tool_form.py
M test/selenium_tests/test_uploads.py
M test/selenium_tests/test_workflow_editor.py
M test/selenium_tests/test_workflow_management.py
M test/selenium_tests/test_workflow_run.py
M test/shed_functional/base/test_db_util.py
M test/shed_functional/base/twilltestcase.py
M test/shed_functional/functional/test_1100_install_updated_repository_dependencies.py
M test/shed_functional/functional/test_1430_repair_installed_repository.py
A test/unit/__init__.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_runner_local.py
M test/unit/managers/base.py
M test/unit/managers/test_CollectionManager.py
M test/unit/managers/test_HistoryContentsManager.py
M test/unit/managers/test_HistoryManager.py
M test/unit/managers/test_UserManager.py
M test/unit/shed_unit/test_installed_repository_manager.py
M test/unit/shed_unit/test_tool_panel_manager.py
M test/unit/test_security_helper.py
M test/unit/tools/test_actions.py
M test/unit/tools/test_collect_primary_datasets.py
M test/unit/tools/test_column_parameters.py
M test/unit/tools/test_data_parameters.py
M test/unit/tools/test_dataset_matcher.py
M test/unit/tools/test_evaluation.py
M test/unit/tools/test_execution.py
M test/unit/tools/test_history_imp_exp.py
M test/unit/tools/test_parameter_parsing.py
M test/unit/tools/test_tool_deps.py
M test/unit/tools/test_tool_loader.py
M test/unit/tools/test_toolbox.py
M test/unit/tools/test_toolbox_filters.py
M test/unit/tools_support.py
M test/unit/unittest_utils/galaxy_mock.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
R test/unit/web/base/__init__.py
R test/unit/web/base/test_HookPluginManager.py
R test/unit/web/base/test_PageServingPluginManager.py
R test/unit/web/base/test_PluginManager.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/workflow_support.py
M tools/data_source/data_source.py
M tools/data_source/fetch.py
M tools/data_source/genbank.py
M tools/data_source/import.py
M tools/data_source/microbial_import.py
M tools/data_source/microbial_import_code.py
M tools/data_source/upload.py
M tools/data_source/upload.xml
M tools/evolution/codingSnps_filter.py
M tools/extract/extract_genomic_dna.py
M tools/extract/liftOver_wrapper.py
M tools/extract/liftOver_wrapper.xml
M tools/filters/axt_to_lav.py
M tools/filters/bed_to_gff_converter.py
M tools/filters/catWrapper.py
M tools/filters/convert_characters.py
M tools/filters/gff/extract_GFF_Features.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/filters/gff_to_bed_converter.py
M tools/filters/gtf_to_bedgraph_converter.py
M tools/filters/join.py
M tools/filters/joiner.xml
M tools/filters/lav_to_bed_code.py
M tools/filters/mergeCols.py
M tools/filters/sff_extract.py
M tools/filters/ucsc_gene_bed_to_exon_bed.py
M tools/filters/ucsc_gene_bed_to_exon_bed.xml
M tools/filters/ucsc_gene_bed_to_intron_bed.py
M tools/filters/ucsc_gene_table_to_intervals.py
M tools/genomespace/genomespace_importer.py
M tools/maf/maf_by_block_number.py
M tools/maf/maf_filter.py
M tools/maf/maf_limit_size.py
M tools/maf/maf_limit_to_species.py
M tools/maf/maf_reverse_complement.py
M tools/maf/maf_stats.py
M tools/maf/maf_thread_for_species.py
M tools/maf/maf_to_bed.py
M tools/maf/vcf_to_maf_customtrack.py
M tools/metag_tools/blat_wrapper.py
M tools/metag_tools/shrimp_color_wrapper.py
M tools/metag_tools/shrimp_wrapper.py
M tools/next_gen_conversion/solid2fastq.py
M tools/plotting/bar_chart.py
M tools/solid_tools/maq_cs_wrapper.py
M tools/solid_tools/solid_qual_stats.py
M tools/sr_assembly/velvetg_wrapper.py
M tools/sr_mapping/bfast_wrapper.py
M tools/stats/aggregate_scores_in_intervals.py
M tools/stats/filtering.py
M tools/stats/grouping.py
M tools/stats/gsummary.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'upstream/dev' into pysam012
Commit: 5581d270e7b921419f89d70ccda5c9d3eabe417b
https://github.com/galaxyproject/galaxy/commit/5581d270e7b921419f89d70ccda5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-06 (Mon, 06 Nov 2017)
Changed paths:
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
Log Message:
-----------
All the way to 0.13 for pysam.
Commit: a2c164a53ad99a0815cd3dbcc0b0b44605d4cfc2
https://github.com/galaxyproject/galaxy/commit/a2c164a53ad99a0815cd3dbcc0b0…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/datatypes/converters/bgzip.py
M lib/galaxy/datatypes/converters/interval_to_tabix_converter.py
M lib/galaxy/datatypes/converters/tabular_to_dbnsfp.py
M lib/galaxy/datatypes/converters/vcf_to_vcf_bgzip.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/visualization/data_providers/genome.py
Log Message:
-----------
Merge pull request #4497 from dannon/pysam012
Bumping pysam to 0.13 *core*, without customization
Compare: https://github.com/galaxyproject/galaxy/compare/7722fbaaad29...a2c164a53ad9
1
0
13 Nov '17
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 4f92759c4930bbaac79dbede0ac7a19b6a6d8580
https://github.com/galaxyproject/galaxy/commit/4f92759c4930bbaac79dbede0ac7…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/__init__.py
Log Message:
-----------
Include path in job script integrity errors
Commit: 7722fbaaad29443325c8de8ac66f46375fc717af
https://github.com/galaxyproject/galaxy/commit/7722fbaaad29443325c8de8ac66f…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/util/job_script/__init__.py
Log Message:
-----------
Merge pull request #4991 from nsoranzo/path_in_job_script_integrity_errors
Include path in job script integrity errors
Compare: https://github.com/galaxyproject/galaxy/compare/c7ef71dfc9df...7722fbaaad29
1
0