Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: a58586f0e4973aa6855142222ed8be124add9ad5
https://github.com/galaxyproject/galaxy/commit/a58586f0e4973aa6855142222ed8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths:
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Cleanup SA objects between workflow invocation scheduling attempts.
This would seem to be a fairly serious memory leak in the abstract but I don't have data that it fixes anything. None the less if it gets into dev and the tests seem to pass I'll open a PR to backport it to at least 17.05 and maybe back even more.
Commit: 802c943fff711dbeb6105b8b3ece68bf29cdee9e
https://github.com/galaxyproject/galaxy/commit/802c943fff711dbeb6105b8b3ece…
Author: Eric Rasche <hxr(a)hx42.org>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Merge pull request #5073 from jmchilton/backport_5045
[17.09] Backport #5045
Compare: https://github.com/galaxyproject/galaxy/compare/ff3a6b084931...802c943fff71
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: b476cc4c57ad86c507eba22c88221584a62954a5
https://github.com/galaxyproject/galaxy/commit/b476cc4c57ad86c507eba22c8822…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-23 (Thu, 23 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Fail job if job output collection fails
We now set a non-zero exit code to actually set a job to failed.
I belive this is a reasonable action, and it avoids green, empty datasets
with log messages like:
```
galaxy.jobs.runners ERROR 2017-11-14 13:32:06,469 (19020/860246.torque6.curie.fr) Job output not returned from cluster: [Errno 2] No such file or directory: '/data/users/mvandenb/gx
124/tmp_nfs/jwd/019/19020/galaxy_19020.o'
galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,491 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.o: [Errno 2] No suc
h file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.o'
galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,503 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.e: [Errno 2] No suc
h file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.e'
galaxy.jobs.runners DEBUG 2017-11-14 13:32:06,513 (19020/860246.torque6.curie.fr) Unable to cleanup /data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.ec: [Errno 2] No su
ch file or directory: '/data/users/mvandenb/gx124/tmp_nfs/jwd/019/19020/galaxy_19020.ec'
```
Commit: 73454e12df8b8fe05aefc8ae120286e976985db8
https://github.com/galaxyproject/galaxy/commit/73454e12df8b8fe05aefc8ae1202…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-27 (Mon, 27 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Fix undefined exit_code_str problem (thx @nsoranzo)
Commit: cacd6eadc5b95686173c9394f635d5a25527f503
https://github.com/galaxyproject/galaxy/commit/cacd6eadc5b95686173c9394f635…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Mark job wrapper as failed in a more direct way
Commit: 13f6eeecf099316acc586282773316f3858c0549
https://github.com/galaxyproject/galaxy/commit/13f6eeecf099316acc5862827733…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
Log Message:
-----------
Add new runner state for 'Job output not returned from cluster'
This would allow adimns to write resubmit conditions for this specific failure.
Commit: fac65894d3efd339ae0449300fba162d177efaed
https://github.com/galaxyproject/galaxy/commit/fac65894d3efd339ae0449300fba…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
Log Message:
-----------
Merge pull request #5078 from mvdbeek/fail_if_job_output_collection_fails
Fail job if job output collection fails
Compare: https://github.com/galaxyproject/galaxy/compare/c6c55e1046a7...fac65894d3ef
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 36e0e01b6b9da78ae6f37f556385befba513bc14
https://github.com/galaxyproject/galaxy/commit/36e0e01b6b9da78ae6f37f556385…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/model/__init__.py
M lib/galaxy/util/handlers.py
Log Message:
-----------
Run job handlers as uWSGI mules
Commit: 85ea2d272803e174915680be8419e3053c8f947c
https://github.com/galaxyproject/galaxy/commit/85ea2d272803e174915680be8419…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
A lib/galaxy/script/__init__.py
M run.sh
A scripts/get_uwsgi_args.py
M scripts/manage_tool_dependencies.py
Log Message:
-----------
Script reusage and generate uWSGI mule args
Commit: e2e3e5f7d12a2f862595b380bf9da12b3b201333
https://github.com/galaxyproject/galaxy/commit/e2e3e5f7d12a2f862595b380bf9d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/model/__init__.py
M lib/galaxy/util/handlers.py
M lib/galaxy/web/stack/__init__.py
A lib/galaxy/web/stack/uwsgi_mule/handler.py
M scripts/get_uwsgi_args.py
Log Message:
-----------
WIP job handlers as uWSGI mules from GCC 2017 Hackathon.
Commit: 092a6b49230c65bc93070d9a388105ac568058dd
https://github.com/galaxyproject/galaxy/commit/092a6b49230c65bc93070d9a3881…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/script/__init__.py
M lib/galaxy/util/handlers.py
M lib/galaxy/web/stack/__init__.py
R lib/galaxy/web/stack/uwsgi_mule/handler.py
M run.sh
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
Log Message:
-----------
WIP uWSGI mule job handlers - it works!
Commit: c7663a4e2e24536f1f3257186de86144399142d2
https://github.com/galaxyproject/galaxy/commit/c7663a4e2e24536f1f3257186de8…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/web/stack/__init__.py
A lib/galaxy/web/stack/message.py
A lib/galaxy/web/stack/transport.py
Log Message:
-----------
WIP job handlers as uWSGI mules refactor
Commit: a06d6cf6167f1ce9aee9a34a28aa50473d19cb35
https://github.com/galaxyproject/galaxy/commit/a06d6cf6167f1ce9aee9a34a28aa…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/util/handlers.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/message.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/galaxy/buildapp.py
Log Message:
-----------
WIP: Job handlers as UWSGI mules, attempt at unprogrammed mules.
Commit: ece3f242fb857a1363a0d143fd62033de4ce9e63
https://github.com/galaxyproject/galaxy/commit/ece3f242fb857a1363a0d143fd62…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
Log Message:
-----------
Abandoning unprogrammed mules (for now), fixes for programmed mules
Commit: 27a0b1ba40dfdf44b3e92ec09b4733df9563103e
https://github.com/galaxyproject/galaxy/commit/27a0b1ba40dfdf44b3e92ec09b47…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/manager.py
A lib/galaxy/util/configdict.py
M lib/galaxy/util/handlers.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
Log Message:
-----------
WIP: attempted to support workers shared between pools, but locking
won't allow for this, since you can't wait on messages from a specific
farm.
Commit: d7dd9b2b6590a3ecddb2bbacec9130a3dbf9e4e2
https://github.com/galaxyproject/galaxy/commit/d7dd9b2b6590a3ecddb2bbacec91…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/app.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/manager.py
R lib/galaxy/util/configdict.py
M lib/galaxy/util/handlers.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/message.py
M lib/galaxy/web/stack/transport.py
M scripts/get_uwsgi_args.py
Log Message:
-----------
WIP: drop stack configurability, this will come later. Cleanup for WIP
PR
Commit: 68542b615c70c7d85885827f42ecfc8521155bbf
https://github.com/galaxyproject/galaxy/commit/68542b615c70c7d85885827f42ec…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-21 (Mon, 21 Aug 2017)
Changed paths:
M scripts/galaxy-main
Log Message:
-----------
Remove unneeded server_name manipulation from galaxy-main script
Commit: c5bd3d4729b04d30dc94a798659ecc6d34683a06
https://github.com/galaxyproject/galaxy/commit/c5bd3d4729b04d30dc94a798659e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-22 (Tue, 22 Aug 2017)
Changed paths:
M config/workflow_schedulers_conf.xml.sample
M lib/galaxy/jobs/handler.py
M lib/galaxy/web/stack/message.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Support workflow scheduling via stack messaging.
Commit: 03368ef549c37f5f4e4f95f2734246930914a368
https://github.com/galaxyproject/galaxy/commit/03368ef549c37f5f4e4f95f27342…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
M lib/galaxy/jobs/runners/__init__.py
Log Message:
-----------
Start job runner worker threads post fork.
Commit: bb7795bcfd18c64244634418040d0b89605a8c92
https://github.com/galaxyproject/galaxy/commit/bb7795bcfd18c64244634418040d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-24 (Thu, 24 Aug 2017)
Changed paths:
A lib/galaxy/util/facts.py
M lib/galaxy/web/stack/__init__.py
Log Message:
-----------
Generalize the collection of system/application "facts" usable for string templating.
Commit: 14e9dddadec856a1a8aa916b4a4459f5fb487a06
https://github.com/galaxyproject/galaxy/commit/14e9dddadec856a1a8aa916b4a44…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/webapps/galaxy/buildapp.py
M scripts/galaxy-main
Log Message:
-----------
WIP: support log configuration from yaml/json app config with
logging.config.dictConfig. Still working on yaml/json config loading in
the webless app.
Commit: aff0a7460e69b59cba67769040d761ac768032c3
https://github.com/galaxyproject/galaxy/commit/aff0a7460e69b59cba67769040d7…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/util/facts.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/stack/__init__.py
M scripts/galaxy-main
Log Message:
-----------
Finish dictConfig logging feature
Commit: ea70bafa0cf5b4b68a09ea62aeabb24b9ef62878
https://github.com/galaxyproject/galaxy/commit/ea70bafa0cf5b4b68a09ea62aeab…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M lib/galaxy/web/stack/__init__.py
Log Message:
-----------
Fix mule starting under uWSGI with --ini-paste
Commit: 17ea3d671facb06ec9a1101f80505c5c64758fe7
https://github.com/galaxyproject/galaxy/commit/17ea3d671facb06ec9a1101f8050…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M run.sh
M scripts/get_uwsgi_args.py
Log Message:
-----------
Improve automatic uWSGI startup options interaction with [uwsgi] section
in config file
Commit: 1326a4d67107206babd4acd457734511f24a8996
https://github.com/galaxyproject/galaxy/commit/1326a4d67107206babd4acd45773…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/util/facts.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/workflow/scheduling_manager.py
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
M test/unit/jobs/test_job_configuration.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Cleaning, lint and test fixes.
Commit: 4d962d4ad29bfdad7c6f108d0300c79354d01a01
https://github.com/galaxyproject/galaxy/commit/4d962d4ad29bfdad7c6f108d0300…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M scripts/get_uwsgi_args.py
Log Message:
-----------
Only include --paste-logger in uWSGI args if logging is configured in
the PasteDeploy config
Commit: bcfa874158bb82b7c45f8ff51d0701cb7b734f06
https://github.com/galaxyproject/galaxy/commit/bcfa874158bb82b7c45f8ff51d07…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-28 (Mon, 28 Aug 2017)
Changed paths:
M scripts/get_uwsgi_args.py
Log Message:
-----------
Fix for job_handler_count = 0
Commit: 9da850289f0d403ccba565ab88123c942db5b491
https://github.com/galaxyproject/galaxy/commit/9da850289f0d403ccba565ab8812…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Allow test framework to run uwsgi tests.
Commit: 5c01c1cc3b71dbc069e03639c4804f084bdb37dc
https://github.com/galaxyproject/galaxy/commit/5c01c1cc3b71dbc069e03639c480…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M test/base/driver_util.py
M test/base/integration_util.py
A test/integration/test_mules_as_job_handlers.py
Log Message:
-----------
Add mules integration test and integration test framework updates to support uwsgi.
Commit: ac4d8477177e94b858519d7873beba352aec0431
https://github.com/galaxyproject/galaxy/commit/ac4d8477177e94b858519d7873be…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Fix connection rejected errors for linux when waiting for uwsgi servers in test framework.
Commit: 27e34d5ad93aa1f62ae5d55d3ceed98d2da3dd7b
https://github.com/galaxyproject/galaxy/commit/27e34d5ad93aa1f62ae5d55d3cee…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Do a better job cleaning up uwsgi processes for tests.
Commit: 8fb47a0a2c211b83e31e64557ec04a05dea17f2b
https://github.com/galaxyproject/galaxy/commit/8fb47a0a2c211b83e31e64557ec0…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-30 (Wed, 30 Aug 2017)
Changed paths:
M test/integration/test_mules_as_job_handlers.py
Log Message:
-----------
Fix mules test to not require ``app`` in test's memory.
Just run a simple upload using a DatasetPopulator instead of running a tool test that requires the tool be in memory.
Commit: 1fe9883774f53f0a03418021eebd78c86978e8b6
https://github.com/galaxyproject/galaxy/commit/1fe9883774f53f0a03418021eebd…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Be a more forceful about cleaning uwsgi during tests.
Commit: 00b8574404dd79e112b22f13ec72043a7b09ab09
https://github.com/galaxyproject/galaxy/commit/00b8574404dd79e112b22f13ec72…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M lib/galaxy/web/stack/__init__.py
Log Message:
-----------
Fix a segfault in uWSGI mules caused by trying to access invalid memory
post-fork. There may be more cases like this that we'll have to handle
in the mule fixup function.
Context
=======
uWSGI mules don't fork()/exec(), they fork() and then (as documented)
run supplied code[1]. In order to read the URL parameter for IGV builds
in the default tool_data_table_conf.xml, Galaxy imports urlopen() from
six.moves.urllib.request. In Python 2.7, this imports the same function
from urllib2. urllib2 uses (and reuses) a module global "opener"
object[2]. This is initialized during the prefork application startup
when used for the IGV data table, and then the same object is used
postfork for the mule to load the same data table.
It was discovered when attempting to run the mule job handler test under
macOS, it does not occur in testing on Linux, nor does it occur on macOS
with the default tool_conf.xml.sample and datatypes_conf.xml.sample.
Whether or not the segfault was encountered seemed to depend on which
tools or datatypes were loaded, but not in any clear pattern. The cause
is presumably due to differences in memory allocation schemes between
macOS and Linux, and perhaps garbage collection differences depending on
different config file sizes? Regardless, it seems to be a classical case
of holding on to references to memory that has been deallocated
elsewhere.
The segfault is specifically on the socket_getaddrinfo function in the
_socket C module that provides functionality for the socket module in
the standard Python lib. socket.getaddrinfo() is called by urlopen() by
way of httplib.
uWSGI mule debugging
--------------------
I ultimately figured out the cause of the segfault with lldb. To make
that experience better, I used a debug build of both Python and uWSGI
(uWSGI was probably less important to do but that process is explained
here anyway). Python with debugging is not ABI compatible with non-debug
Python, so building all of Galaxy's C Extension wheels was necessary. In
many cases, pip will do this for you (using the standard pip invocation
in scripts/common_startup.sh), but not all will be successful. To build
debug Python and debug uWSGI and run Galaxy under them, I used the
following steps:
1. You will need a newer version OpenSSL than the one that ships with
Sierra, I used the one from Brew:
CFLAGS=-I/usr/local/opt/openssl/include \
LDFLAGS=-L/usr/local/opt/openssl/lib \
MACOSX_DEPLOYMENT_TARGET=10.12 \
./configure --prefix=$HOME/pydebug --with-pydebug
Be sure to set $MACOSX_DEPLOYMENT_TARGET. If you do not, the
`getaddrinfo` function will utilize locking around `getaddrinfo` that
should not be used[3].
2. After intsalling Python, `virtualenv -p ~/pydebug .venv` in the
Galaxy root.
3. In the uWSGI source, copy buildconf/default.ini to
buildconf/debug.ini, set `debug = true` in debug.ini and then (with
.venv activated) run:
UWSGI_PROFILE=buildconf/debug.ini python setup.py install
4. Manually install a few problematic dependencies:
- Use the Starforge recipe for building pysam[4], which mainly means
grabbing a tarball of @dannon's fork, fixing the version number,
and running `python setup.py install`. The ssdist tarball for this
verison on wheels.galaxyproject.org is broken (files are missing
from its manifest) and I need to fix that. Dannon is also currently
working on upstreaming his changes and updating Galaxy for the
latest version of pysam so this shouldn't be a problem in the
future.
- The mercurial sdist tarball on wheels.galaxyproject.org is also
broken, download the correct version tarball directly from the
mercurial release distribution site and `python setup.py install`
it. I need to fix this as well.
- Install numpy before bx-python (if it's not installed before bx is,
bx will be missing needed features):
pip install -i https://wheels.galaxyproject.org --no-binary :all: \
$(grep -i numpy= requirements.txt)
5. Install remaining requirements, iirc the rest should be ok:
pip install -i https://wheels.galaxyproject.org --no-binary :all: \
-r requirements.txt
--no-binary :all: is necessary because there are numerous macOS
wheels in PyPI with a `none` SOABI tag, meaning these wheels will
install but will not work for the debug Python ABI.
When you run Galaxy under the debugger, you won't be able to directly
control the fork()ed mules. Instead, you'll need to fire up a second
debugger to catch the mule[5]:
1. Start up Galaxy under lldb, set a breakpoint on fork Be sure that
your virtualenv is *NOT* activated before starting lldb, or it will
fail miserably at loading its own python module.
% lldb .venv/bin/uwsgi
(lldb) b fork
2. Run Galaxy, e.g.:
(lldb) r --virtualenv /Users/nate/galaxy/.venv --module galaxy.webapps.galaxy.buildapp:uwsgi_app_factory() --yaml config/galaxy.yml --processes 1 --threads 4 --http localhost:8080 --pythonpath lib --master --static-map /static/style=/Users/nate/galaxy/static/style/blue --static-map /static=/Users/nate/galaxy/static --die-on-term --enable-threads --py-call-osafterfork --mule=lib/galaxy/main.py --farm=job-handlers:1
3. The first fork() is for the workers, so you'll want to skip this:
(lldb) n
4. The second fork is for the mule. At this point, start a second lldb
in another terminal, set a breakpoint on something interesting, and
attach it to the process that is about to start:
% lldb
(lldb) b socket_getaddrinfo
(lldb) pro at -n uwsgi -w
5. Continue the fork in the original lldb:
(lldb) n
6. Continue debugging in the second lldb, which is now attached to the
mule.
[1]: https://github.com/unbit/uwsgi/blob/5039a4b679735348422638baa7cff7a8116762e…
[2]: https://github.com/python/cpython/blob/20958e6d91d11a80d6c664ce6346791259b1…
[3]: https://emptysqua.re/blog/getaddrinfo-deadlock/
[4]: https://github.com/galaxyproject/starforge/blob/f1013ddf6119381ffba6df06e8d…
[5]: https://stackoverflow.com/questions/14746315/how-to-attach-to-child-process…
Commit: e91db56f0e377f94574f80c833182e79a43156fb
https://github.com/galaxyproject/galaxy/commit/e91db56f0e377f94574f80c83318…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Use fancy uWSGI log messages when running tests under uWSGI, or you can
set whatever log format string you want with `$GALAXY_TEST_LOG_FORMAT`.
If unset, and not running under uWSGI, galaxy.config.logging (the
logging.config.dictConfig dict) will not be set and the default logging
config will be used.
Commit: 3477906dc556ce17223bafbc470f1d809f6196cb
https://github.com/galaxyproject/galaxy/commit/3477906dc556ce17223bafbc470f…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M lib/galaxy/tools/toolbox/base.py
Log Message:
-----------
Provide failure reason when tool configs fail to load due to system
errors (ENOENT, EPERM, etc.).
Commit: 3f0082515af630bd095ee5fc57bac044369c8f0e
https://github.com/galaxyproject/galaxy/commit/3f0082515af630bd095ee5fc57ba…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-08-31 (Thu, 31 Aug 2017)
Changed paths:
M test/base/driver_util.py
A test/functional/tools/config_vars.xml
M test/functional/tools/samples_tool_conf.xml
M test/integration/test_mules_as_job_handlers.py
Log Message:
-----------
Improvements for mule job handler testing. Ensure that the server
running the job is a mule. Added a test tool that will write Galaxy
app.config attributes to the output dataset.
Commit: 09feaf6f4d46509c7401970013b5a8097a5d4c4e
https://github.com/galaxyproject/galaxy/commit/09feaf6f4d46509c7401970013b5…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/script/__init__.py
M lib/galaxy/util/__init__.py
A lib/galaxy/util/path.py
M lib/galaxy/util/properties.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/stack/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/util/commit_util.py
M run.sh
M run_reports.sh
M run_tool_shed.sh
M scripts/common_startup_functions.sh
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
M test/base/driver_util.py
Log Message:
-----------
- Do all logging configuration other than paste fileConfig logging from
dictConfig. Default log message format varies by stack.
- Refactor a lot of file extension handling in to galaxy.util.path.
- Simplify and improve config file finding.
- Simplify and improve native app creation.
- Integrate uWSGI argument generation with @jmchilton's improvements to
the startup scripts.
- Fix starting without a config file under uWSGI
Commit: 11857db011f4814a4aa0feb151a8a838f91b8c88
https://github.com/galaxyproject/galaxy/commit/11857db011f4814a4aa0feb151a8…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Attempt uWSGI restarts when running for testing. It's not able to detect
if it failed due to port binding, but it'll retry if uwsgi exits
non-zero.
Commit: 318bf0bd01ffe6a2bd08fbbfffd8be88e95ae8f7
https://github.com/galaxyproject/galaxy/commit/318bf0bd01ffe6a2bd08fbbfffd8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Rework cleanup of uwsgi in tests...
This looks cleaner and was closer to what I originally wanted - undoes some stuff @natefoo did hopefully he isn't mad.
Commit: 37738b94fbcad6e5aefe410f0c01af4dbac17281
https://github.com/galaxyproject/galaxy/commit/37738b94fbcad6e5aefe410f0c01…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-01 (Fri, 01 Sep 2017)
Changed paths:
M test/integration/test_mules_as_job_handlers.py
Log Message:
-----------
More mule testing.
Commit: 1e6080e1bf6d410a617079af93e85a29cad21243
https://github.com/galaxyproject/galaxy/commit/1e6080e1bf6d410a617079af93e8…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-02 (Sat, 02 Sep 2017)
Changed paths:
M test/base/driver_util.py
Log Message:
-----------
Don't require integration tests to use the same port for every Galaxy instance.
The previous logic would pick a port at random if one wasn't explicitly defined and then set an environment variable requiring each instance to re-use that. This new logic doesn't reuse randomly assigned ports that way by tracking if a port was randomly assigned or not.
Commit: 32a280bf3100f359e1d046206d47a36e0d92db62
https://github.com/galaxyproject/galaxy/commit/32a280bf3100f359e1d046206d47…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-09-03 (Sun, 03 Sep 2017)
Changed paths:
M test/base/integration_util.py
M test/integration/test_mules_as_job_handlers.py
Log Message:
-----------
Just skip the mule tests on Jenkins.
They work locally alone or ran together, they work locally in the same Docker container as Jenkins, I don't understand.
Commit: d7aec7e04dc064fd9e133d9a592e1cb5ef486037
https://github.com/galaxyproject/galaxy/commit/d7aec7e04dc064fd9e133d9a592e…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-09 (Thu, 09 Nov 2017)
Changed paths:
M test/base/integration_util.py
M test/integration/test_mules_as_job_handlers.py
Log Message:
-----------
Revert "Just skip the mule tests on Jenkins."
This reverts commit 32a280bf3100f359e1d046206d47a36e0d92db62.
Commit: 30266c522127d4b9b13fd0a7433473747cec023c
https://github.com/galaxyproject/galaxy/commit/30266c522127d4b9b13fd0a74334…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-09 (Thu, 09 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
M README.rst
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/jqtouch.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
A 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/dataset.less
M client/galaxy/style/less/galaxy_bootstrap/variables.less
M client/galaxy/style/less/galaxy_variables.less
R client/galaxy/style/less/iphone.less
M client/galaxy/style/less/library.less
A client/galaxy/style/less/theme/plain.less
M client/galaxy/style/less/trackster.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/dependency_resolvers_conf.xml.sample
M config/error_report.yml.sample
M config/galaxy.ini.sample
A config/lmod_modules_mapping.yml.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
A config/plugins/interactive_environments/hicbrowser/config/allowed_images.yml.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.ini.sample
A config/plugins/interactive_environments/hicbrowser/config/hicbrowser.xml
A config/plugins/interactive_environments/hicbrowser/static/js/hicbrowser.js
A 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/admin/special_topics/bug_reports.rst
A doc/source/dev/finding_and_improving_slow_code.rst
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
R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.py
R lib/galaxy/datatypes/converters/bcf_bgzip_to_bcf_converter.xml
R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.py
R lib/galaxy/datatypes/converters/bcf_to_bcf_bgzip_converter.xml
A lib/galaxy/datatypes/converters/bcf_to_bcf_uncompressed_converter.xml
A lib/galaxy/datatypes/converters/bcf_uncompressed_to_bcf_converter.xml
M lib/galaxy/datatypes/converters/bed_to_gff_converter.py
A lib/galaxy/datatypes/converters/biom1_to_biom2.xml
A lib/galaxy/datatypes/converters/biom2_to_biom1.xml
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/set_metadata_tool.xml
M lib/galaxy/datatypes/sniff.py
M lib/galaxy/datatypes/tabular.py
A lib/galaxy/datatypes/test/1.bcf
A lib/galaxy/datatypes/test/1.bcf_uncompressed
A lib/galaxy/datatypes/test/biom2_sparse_otu_table_hdf5.biom
A lib/galaxy/datatypes/test/chebi_57262.v3k.mol
A lib/galaxy/datatypes/test/example.iqtree
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
M lib/galaxy/datatypes/text.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/generic_util.py
M lib/galaxy/dependencies/__init__.py
M lib/galaxy/dependencies/conditional-requirements.txt
A lib/galaxy/dependencies/dev-requirements.txt
R lib/galaxy/dependencies/dev-requirements.txt
M lib/galaxy/dependencies/pinned-requirements.txt
A lib/galaxy/dependencies/pipfiles/develop/Pipfile
A lib/galaxy/dependencies/pipfiles/develop/Pipfile.lock
A lib/galaxy/dependencies/pipfiles/develop/pinned-hashed-requirements.txt
A lib/galaxy/dependencies/pipfiles/develop/pinned-requirements.txt
A lib/galaxy/dependencies/pipfiles/flake8/Pipfile
A lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
A lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt
A lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
A lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile
A lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock
A lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt
A lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt
A lib/galaxy/dependencies/pipfiles/update.sh
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/external_services/actions.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/jobs/command_factory.py
M lib/galaxy/jobs/deferred/__init__.py
M lib/galaxy/jobs/deferred/pacific_biosciences_smrt_portal.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/output_checker.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/condor.py
M lib/galaxy/jobs/runners/drmaa.py
M lib/galaxy/jobs/runners/godocker.py
M lib/galaxy/jobs/runners/kubernetes.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/pbs.py
M lib/galaxy/jobs/runners/pulsar.py
M lib/galaxy/jobs/runners/slurm.py
M lib/galaxy/jobs/runners/state_handler_factory.py
M lib/galaxy/jobs/runners/state_handlers/_safe_eval.py
M lib/galaxy/jobs/runners/tasks.py
M lib/galaxy/jobs/runners/util/cli/job/slurm.py
M lib/galaxy/jobs/runners/util/cli/job/torque.py
M lib/galaxy/jobs/runners/util/cli/shell/rsh.py
M lib/galaxy/jobs/runners/util/job_script/DEFAULT_JOB_FILE_TEMPLATE.sh
M lib/galaxy/jobs/runners/util/job_script/__init__.py
M lib/galaxy/jobs/runners/util/kill.py
M lib/galaxy/jobs/transfer_manager.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/collections_util.py
M lib/galaxy/managers/context.py
M lib/galaxy/managers/folders.py
A lib/galaxy/managers/jobs.py
M lib/galaxy/managers/libraries.py
A lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/custom_types.py
M lib/galaxy/model/item_attrs.py
M lib/galaxy/model/mapping.py
M lib/galaxy/model/metadata.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py
M lib/galaxy/model/migrate/versions/0024_page_slug_unique_constraint.py
M lib/galaxy/model/migrate/versions/0032_stored_workflow_slug_column.py
M lib/galaxy/model/migrate/versions/0033_published_cols_for_histories_and_workflows.py
M lib/galaxy/model/migrate/versions/0041_workflow_invocation.py
M lib/galaxy/model/migrate/versions/0042_workflow_invocation_fix.py
M lib/galaxy/model/migrate/versions/0056_workflow_outputs.py
M lib/galaxy/model/migrate/versions/0061_tasks.py
M lib/galaxy/model/migrate/versions/0076_fix_form_values_data_corruption.py
M lib/galaxy/model/migrate/versions/0115_longer_user_password_field.py
M lib/galaxy/model/search.py
M lib/galaxy/model/tool_shed_install/__init__.py
M lib/galaxy/model/tool_shed_install/migrate/check.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pulsar.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/queue_worker.py
M lib/galaxy/sample_tracking/external_service_types.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/security/__init__.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/actions/upload_common.py
M lib/galaxy/tools/cache.py
M lib/galaxy/tools/data/__init__.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_compat.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/container_resolvers/mulled.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_channel.py
M lib/galaxy/tools/deps/requirements.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
A lib/galaxy/tools/deps/resolvers/lmod.py
M lib/galaxy/tools/deps/resolvers/modules.py
M lib/galaxy/tools/deps/resolvers/resolver_mixins.py
M lib/galaxy/tools/deps/resolvers/tool_shed_packages.py
M lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py
A lib/galaxy/tools/error_reports/plugins/github.py
A lib/galaxy/tools/error_reports/plugins/influxdb.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/evaluation.py
M lib/galaxy/tools/flatten_collection.xml
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/imp_exp/unpack_tar_gz_archive.py
M lib/galaxy/tools/linters/help.py
M lib/galaxy/tools/loader.py
M lib/galaxy/tools/loader_directory.py
M lib/galaxy/tools/locations/dockstore.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/grouping.py
M lib/galaxy/tools/parameters/input_translation.py
M lib/galaxy/tools/parameters/meta.py
M lib/galaxy/tools/parameters/sanitize.py
M lib/galaxy/tools/parameters/validation.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/output_actions.py
M lib/galaxy/tools/parser/output_objects.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/parser.py
M lib/galaxy/tools/util/maf_utilities.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/wrappers.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
R lib/galaxy/util/backports/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/checkers.py
M lib/galaxy/util/compression_utils.py
M lib/galaxy/util/dictifiable.py
M lib/galaxy/util/handlers.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/heartbeat.py
M lib/galaxy/util/image_util.py
M lib/galaxy/util/jstree.py
R lib/galaxy/util/log/__init__.py
R lib/galaxy/util/log/fluent_log.py
A lib/galaxy/util/logging/__init__.py
A lib/galaxy/util/logging/fluent_log.py
A lib/galaxy/util/monitors.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/serve.py
A lib/galaxy/util/path/__init__.py
A lib/galaxy/util/path/ntpath.py
A lib/galaxy/util/path/posixpath.py
M lib/galaxy/util/plugin_config.py
M lib/galaxy/util/properties.py
M lib/galaxy/util/sanitize_html.py
M lib/galaxy/util/streamball.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/version.py
M lib/galaxy/visualization/data_providers/basic.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/genomes.py
A lib/galaxy/visualization/plugins/interactive_environments.py
M lib/galaxy/visualization/plugins/plugin.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/web/base/controller.py
R lib/galaxy/web/base/interactive_environments.py
R lib/galaxy/web/base/pluginframework.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/base.py
M lib/galaxy/web/framework/decorators.py
M lib/galaxy/web/framework/helpers/grids.py
M lib/galaxy/web/framework/middleware/error.py
M lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/web/framework/middleware/sentry.py
M lib/galaxy/web/framework/middleware/statsd.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/authenticate.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/group_roles.py
M lib/galaxy/webapps/galaxy/api/group_users.py
M lib/galaxy/webapps/galaxy/api/groups.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/jobs.py
R lib/galaxy/webapps/galaxy/api/lda_datasets.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
A lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
R lib/galaxy/webapps/galaxy/api/request_types.py
R lib/galaxy/webapps/galaxy/api/requests.py
M lib/galaxy/webapps/galaxy/api/roles.py
R lib/galaxy/webapps/galaxy/api/samples.py
M lib/galaxy/webapps/galaxy/api/tool_data.py
M lib/galaxy/webapps/galaxy/api/users.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/galaxy/config_watchers.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/async.py
M lib/galaxy/webapps/galaxy/controllers/dataset.py
R lib/galaxy/webapps/galaxy/controllers/external_service.py
R lib/galaxy/webapps/galaxy/controllers/external_services.py
M lib/galaxy/webapps/galaxy/controllers/forms.py
M lib/galaxy/webapps/galaxy/controllers/history.py
M lib/galaxy/webapps/galaxy/controllers/library.py
M lib/galaxy/webapps/galaxy/controllers/library_common.py
R lib/galaxy/webapps/galaxy/controllers/mobile.py
M lib/galaxy/webapps/galaxy/controllers/page.py
R lib/galaxy/webapps/galaxy/controllers/request_type.py
R lib/galaxy/webapps/galaxy/controllers/requests.py
R lib/galaxy/webapps/galaxy/controllers/requests_admin.py
R lib/galaxy/webapps/galaxy/controllers/requests_common.py
M lib/galaxy/webapps/galaxy/controllers/root.py
M lib/galaxy/webapps/galaxy/controllers/tool_runner.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/buildapp.py
M lib/galaxy/webapps/reports/config.py
M lib/galaxy/webapps/reports/controllers/system.py
M lib/galaxy/webapps/reports/controllers/tools.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/controllers/upload.py
M lib/galaxy/webapps/tool_shed/model/__init__.py
M lib/galaxy/webapps/tool_shed/model/migrate/check.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0001_initial_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0002_add_tool_suite_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0003_review_and_review_association_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0004_repository_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0005_drop_tool_related_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0006_add_email_alerts_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0007_add_long_description_times_downloaded_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0008_add_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0009_add_malicious_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0010_add_new_repo_alert_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0011_add_tool_versions_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0012_add_downloadable_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0013_add_review_tables.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0014_add_deprecated_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0015_add_api_keys_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0016_add_do_not_test_tools_functionally_correct_errors_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0017_add_galaxy_utility_columns_to_repository_metadata_table.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0018_add_repository_metadata_flag_columns.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0019_add_skip_tool_test_table_and_test_install_error_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0020_add_repository_type_column.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0021_change_repository_type_value.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0022_add_repository_admin_roles.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0023_add_repository_url_and_hompeage_url.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0024_password_reset.py
M lib/galaxy/webapps/tool_shed/model/migrate/versions/0025_session_timeout.py
M lib/galaxy/webapps/tool_shed/search/repo_search.py
M lib/galaxy/webhooks/__init__.py
M lib/galaxy/work/context.py
M lib/galaxy/workflow/modules.py
M lib/galaxy/workflow/run.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/galaxy_ext/metadata/set_metadata.py
M lib/mimeparse.py
M lib/psyco_full.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py
M lib/tool_shed/galaxy_install/installed_repository_manager.py
M lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py
M lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/tag_handler.py
M lib/tool_shed/grids/repository_grids.py
M lib/tool_shed/grids/util.py
M lib/tool_shed/managers/groups.py
M lib/tool_shed/metadata/metadata_generator.py
M lib/tool_shed/metadata/repository_metadata_manager.py
M lib/tool_shed/tool_shed_registry.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/util/admin_util.py
M lib/tool_shed/util/basic_util.py
M lib/tool_shed/util/commit_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/util/workflow_util.py
M lib/tool_shed/util/xml_util.py
M manage_db.sh
M manage_tools.sh
M run_tests.sh
M scripts/api/copy_hda_to_library_folder.py
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M scripts/loc_files/create_all_fasta_loc.py
M scripts/manage_tool_dependencies.py
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M scripts/metagenomics/convert_title.py
M scripts/microbes/BeautifulSoup.py
M scripts/microbes/create_bacteria_loc_file.py
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M scripts/microbes/harvest_bacteria.py
M scripts/microbes/ncbi_to_ucsc.py
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M scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py
M scripts/tool_shed/build_ts_whoosh_index.py
M scripts/tool_shed/check_download_urls.py
M scripts/tool_shed/check_filesystem_for_empty_tool_dependency_installation_paths.py
M scripts/tool_shed/check_s3_for_empty_tool_dependency_installation_paths.py
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M scripts/tools/maf/check_loc_file.py
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M setup.cfg
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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
M static/scripts/mvc/toolshed/repository-view.js
R static/scripts/mvc/toolshed/shed-category-view.js
M static/scripts/mvc/toolshed/shed-list-view.js
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
M static/scripts/mvc/upload/default/default-row.js
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
A 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
M static/scripts/mvc/workflow/workflow-view-terminals.js
M static/scripts/mvc/workflow/workflow-view.js
M static/scripts/mvc/workflow/workflow.js
M static/scripts/nls/de/locale.js
M static/scripts/nls/es/locale.js
M static/scripts/nls/fr/locale.js
M static/scripts/nls/ja/locale.js
M static/scripts/nls/locale.js
M static/scripts/nls/zh/locale.js
M static/scripts/onload.js
R static/scripts/packed
M static/scripts/polyfills.js
M static/scripts/reports_webapp/run_stats.js
M static/scripts/ui/autocom_tagging.js
M static/scripts/ui/editable-text.js
M static/scripts/ui/fa-icon-button.js
M static/scripts/ui/filter-control.js
M static/scripts/ui/hoverhighlight.js
M static/scripts/ui/loading-indicator.js
M static/scripts/ui/mode-button.js
M static/scripts/ui/pagination.js
M static/scripts/ui/peek-column-selector.js
M static/scripts/ui/popupmenu.js
M static/scripts/ui/scroll-panel.js
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
M static/scripts/viz/trackster/slotting.js
M static/scripts/viz/trackster/tracks.js
M static/scripts/viz/trackster/util.js
M static/scripts/viz/visualization.js
M static/scripts/viz/viz_views.js
M static/style/blue/base.css
R static/style/blue/iphone.css
M static/style/blue/library.css
M static/style/blue/trackster.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
M static/toolshed/maps/mvc/groups/group-model.js.map
M static/toolshed/scripts/mvc/groups/group-detail-view.js
M static/toolshed/scripts/mvc/groups/group-list-view.js
M static/toolshed/scripts/mvc/groups/group-listrow-view.js
M static/toolshed/scripts/mvc/groups/group-model.js
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
R templates/admin/request_type/create_request_type.mako
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/copy_view.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/mobile/dataset/detail.mako
R templates/webapps/galaxy/mobile/dataset/peek.mako
R templates/webapps/galaxy/mobile/form.mako
R templates/webapps/galaxy/mobile/history/detail.mako
R templates/webapps/galaxy/mobile/history/list.mako
R templates/webapps/galaxy/mobile/index.mako
R templates/webapps/galaxy/mobile/manage_library.mako
R templates/webapps/galaxy/mobile/settings.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/reports/run_stats.mako
M templates/webapps/tool_shed/group/index.mako
A test-data/joiner_header_in1.tab
A test-data/joiner_header_in2.tab
A test-data/joiner_out1.bed
A test-data/joiner_out2.bed
A test-data/joiner_out3.bed
A test-data/joiner_out4.bed
A test-data/joiner_out5.tab
A test-data/joiner_out6.tab
A test-data/joiner_out7.tab
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_libraries.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/interactor.py
M test/base/populators.py
R test/base/test_db_util.py
A test/base/testcase.py
M test/base/tool_shed_util.py
R test/base/twilltestcase.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
R test/functional/database_contexts.py
R test/functional/test_library_templates.py
M test/functional/test_toolbox.py
M test/functional/tools/collection_split_on_column.xml
M test/functional/tools/composite.xml
M test/functional/tools/composite_output.xml
M test/functional/tools/composite_output_tests.xml
A test/functional/tools/data_source.py
A test/functional/tools/empty_datasets.xml
M test/functional/tools/metadata.xml
M test/functional/tools/sample_datatypes_conf.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/tools/test_data_source.xml
A 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/driver_factory.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
M test/galaxy_selenium/sizzle.py
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
A test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_registration.py
A test/selenium_tests/test_saved_histories.py
A 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/config/1607_root_filters/config/galaxy.ini
M test/unit/config/1607_root_samples/config/galaxy.ini
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_conda_resolution.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.xml
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 'origin/dev' into job-handler-mules
Commit: 4eface7e722ff46276225457da0dcacc537fb10e
https://github.com/galaxyproject/galaxy/commit/4eface7e722ff46276225457da0d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-09 (Thu, 09 Nov 2017)
Changed paths:
R lib/galaxy/util/path.py
M lib/galaxy/util/path/__init__.py
Log Message:
-----------
Fix path module divergence
Commit: b75583ea26269101f12cb29df76a23eeecf68ab5
https://github.com/galaxyproject/galaxy/commit/b75583ea26269101f12cb29df76a…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-09 (Thu, 09 Nov 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/util/properties.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/galaxy/buildapp.py
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
M scripts/manage_tool_dependencies.py
Log Message:
-----------
Fix post-merge lint issues
Commit: bf9e2b6a9696a7b3ecc0b369424c9b805ac64a11
https://github.com/galaxyproject/galaxy/commit/bf9e2b6a9696a7b3ecc0b369424c…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-09 (Thu, 09 Nov 2017)
Changed paths:
M lib/galaxy/util/path/__init__.py
Log Message:
-----------
Fix call to __listify.
Commit: e97de138e32d350d4fc7593498130ca9cd3c9d06
https://github.com/galaxyproject/galaxy/commit/e97de138e32d350d4fc759349813…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-10 (Fri, 10 Nov 2017)
Changed paths:
M test/base/integration_util.py
M test/integration/test_mules_as_job_handlers.py
Log Message:
-----------
Revert "Revert "Just skip the mule tests on Jenkins.""
This reverts commit d7aec7e04dc064fd9e133d9a592e1cb5ef486037.
Commit: b96a8476899aef2dfe1e1b6cde5048afae8e3428
https://github.com/galaxyproject/galaxy/commit/b96a8476899aef2dfe1e1b6cde50…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-10 (Fri, 10 Nov 2017)
Changed paths:
M lib/galaxy/util/properties.py
Log Message:
-----------
Fix an iterator bug with find_config_file() when using include_samples
and write a doctest for it.
Commit: df6a1dedc0c68c8b743b63a6fddaaac71c2b56bc
https://github.com/galaxyproject/galaxy/commit/df6a1dedc0c68c8b743b63a6fdda…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-10 (Fri, 10 Nov 2017)
Changed paths:
M lib/galaxy/model/orm/scripts.py
Log Message:
-----------
Fix config file finding in the orm scripts utility and make its doctest
clean up after itself
Commit: b8df770bfd3d0e3bd2d5cb26db3cf159ed4e8d3a
https://github.com/galaxyproject/galaxy/commit/b8df770bfd3d0e3bd2d5cb26db3c…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-10 (Fri, 10 Nov 2017)
Changed paths:
M lib/galaxy/util/properties.py
M lib/galaxy/web/stack/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
Log Message:
-----------
Fix import linting errors
Commit: cf9ba1e0cc88f695a27d74c96895b3d6b093e583
https://github.com/galaxyproject/galaxy/commit/cf9ba1e0cc88f695a27d74c96895…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M config/galaxy.ini.sample
M lib/galaxy/app.py
M lib/galaxy/util/properties.py
Log Message:
-----------
Clarifications/fixes from @nsoranzo's comments
Commit: b805fa5945e1f6799e6cf28097155e7b1d434b4e
https://github.com/galaxyproject/galaxy/commit/b805fa5945e1f6799e6cf2809715…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/util/__init__.py
M lib/tool_shed/capsule/capsule_manager.py
Log Message:
-----------
Undo changes unrelated to uWSGI mule work
Commit: 806438edc9b3b407b9cb259f7cdaa8a85fe97f64
https://github.com/galaxyproject/galaxy/commit/806438edc9b3b407b9cb259f7cda…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
R lib/galaxy/script/__init__.py
A lib/galaxy/util/script.py
M scripts/get_uwsgi_args.py
M scripts/manage_tool_dependencies.py
Log Message:
-----------
Revert script changes unrelated to uWSGI mule work. Includes
galaxy.util.script so that get_uwsgi_args.py still works, but that will
be PR'd separately and merged later.
Commit: 1062c705a2a7a8e4cb1b8c6899941474a620885d
https://github.com/galaxyproject/galaxy/commit/1062c705a2a7a8e4cb1b8c689994…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-13 (Mon, 13 Nov 2017)
Changed paths:
M lib/galaxy/util/facts.py
Log Message:
-----------
Fix typo in facts module
Commit: c340d4ebecd56583d7b524e380dedf460e5a7175
https://github.com/galaxyproject/galaxy/commit/c340d4ebecd56583d7b524e380de…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M lib/galaxy/model/orm/scripts.py
M lib/tool_shed/galaxy_install/migrate/check.py
R manage_tools.sh
R scripts/manage_tools.py
Log Message:
-----------
Fix tool migrations with config file changes, do everything from
manage_db.sh.
Commit: 418fd53739800b639924455722618b7172e23168
https://github.com/galaxyproject/galaxy/commit/418fd53739800b63992445572261…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
R .ci/flake8_lint_include_list.txt
R .ci/flake8_wrapper_imports.sh
M .ci/jenkins/selenium/run_tests.sh
M .travis.yml
M client/galaxy/scripts/apps/panels/admin-panel.js
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/collection/collection-view.js
M client/galaxy/scripts/mvc/history/hda-li.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
A client/galaxy/scripts/mvc/history/history-item-li.js
M client/galaxy/scripts/mvc/history/history-model.js
M client/galaxy/scripts/mvc/history/history-view.js
M client/galaxy/scripts/mvc/tool/tool-form-base.js
M client/galaxy/scripts/utils/ajax-queue.js
M config/datatypes_conf.xml.sample
M config/galaxy.ini.sample
A config/plugins/interactive_environments/askomics/config/allowed_images.yml.sample
A config/plugins/interactive_environments/askomics/config/askomics.ini.sample
A config/plugins/interactive_environments/askomics/config/askomics.xml
A config/plugins/interactive_environments/askomics/static/js/askomics.js
A config/plugins/interactive_environments/askomics/templates/askomics.mako
M config/plugins/webhooks/demo/tour_generator/static/script.js
M doc/source/releases/17.09_announce.rst
A lib/galaxy/actions/library.py
M lib/galaxy/app.py
M lib/galaxy/auth/__init__.py
M lib/galaxy/auth/providers/ldap_ad.py
M lib/galaxy/auth/providers/pam_auth.py
M lib/galaxy/config.py
M lib/galaxy/dataset_collections/matching.py
M lib/galaxy/dataset_collections/registry.py
M lib/galaxy/dataset_collections/types/list.py
M lib/galaxy/dataset_collections/types/paired.py
M lib/galaxy/datatypes/converters/bgzip.py
A lib/galaxy/datatypes/converters/cram_to_bam.py
A lib/galaxy/datatypes/converters/cram_to_bam_converter.xml
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/datatypes/data.py
M lib/galaxy/datatypes/dataproviders/dataset.py
M lib/galaxy/datatypes/display_applications/application.py
M lib/galaxy/datatypes/graph.py
M lib/galaxy/datatypes/interval.py
M lib/galaxy/datatypes/registry.py
M lib/galaxy/datatypes/sequence.py
M lib/galaxy/datatypes/tabular.py
M lib/galaxy/datatypes/tracks.py
M lib/galaxy/datatypes/util/gff_util.py
M lib/galaxy/dependencies/conda-environment.txt
M lib/galaxy/dependencies/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/Pipfile
M lib/galaxy/dependencies/pipfiles/flake8/Pipfile.lock
M lib/galaxy/dependencies/pipfiles/flake8/pinned-hashed-requirements.txt
M lib/galaxy/dependencies/pipfiles/flake8/pinned-requirements.txt
R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile
R lib/galaxy/dependencies/pipfiles/flake8_imports/Pipfile.lock
R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-hashed-requirements.txt
R lib/galaxy/dependencies/pipfiles/flake8_imports/pinned-requirements.txt
M lib/galaxy/dependencies/pipfiles/update.sh
M lib/galaxy/dependencies/requirements.txt
M lib/galaxy/external_services/actions.py
M lib/galaxy/external_services/service.py
M lib/galaxy/forms/forms.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/dynamic_tool_destination.py
M lib/galaxy/jobs/mapper.py
M lib/galaxy/jobs/metrics/__init__.py
M lib/galaxy/jobs/metrics/collectl/processes.py
M lib/galaxy/jobs/metrics/instrumenters/collectl.py
M lib/galaxy/jobs/metrics/instrumenters/cpuinfo.py
M lib/galaxy/jobs/metrics/instrumenters/meminfo.py
M lib/galaxy/jobs/rule_helper.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/jobs/runners/chronos.py
M lib/galaxy/jobs/runners/cli.py
M lib/galaxy/jobs/runners/local.py
M lib/galaxy/jobs/runners/state_handlers/resubmit.py
M lib/galaxy/jobs/runners/util/__init__.py
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/jobs/splitters/multi.py
M lib/galaxy/managers/citations.py
M lib/galaxy/managers/collections.py
M lib/galaxy/managers/configuration.py
M lib/galaxy/managers/containers.py
M lib/galaxy/managers/datasets.py
M lib/galaxy/managers/folders.py
M lib/galaxy/managers/hdas.py
M lib/galaxy/managers/hdcas.py
M lib/galaxy/managers/histories.py
M lib/galaxy/managers/history_contents.py
M lib/galaxy/managers/library_datasets.py
M lib/galaxy/managers/pages.py
M lib/galaxy/managers/ratable.py
M lib/galaxy/managers/rbac_secured.py
M lib/galaxy/managers/roles.py
M lib/galaxy/managers/sharable.py
M lib/galaxy/managers/tags.py
M lib/galaxy/managers/users.py
M lib/galaxy/managers/visualizations.py
M lib/galaxy/managers/workflows.py
M lib/galaxy/model/__init__.py
M lib/galaxy/model/migrate/check.py
M lib/galaxy/objectstore/__init__.py
M lib/galaxy/objectstore/azure_blob.py
M lib/galaxy/objectstore/pithos.py
M lib/galaxy/objectstore/rods.py
M lib/galaxy/objectstore/s3.py
M lib/galaxy/objectstore/s3_multipart_upload.py
M lib/galaxy/openid/providers.py
M lib/galaxy/queue_worker.py
M lib/galaxy/queues.py
M lib/galaxy/sample_tracking/request_types.py
M lib/galaxy/tools/__init__.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/upload.py
M lib/galaxy/tools/cache.py
M lib/galaxy/tools/cwl/parser.py
M lib/galaxy/tools/cwl/schema.py
M lib/galaxy/tools/deps/__init__.py
M lib/galaxy/tools/deps/conda_util.py
M lib/galaxy/tools/deps/containers.py
M lib/galaxy/tools/deps/mulled/mulled_build.py
M lib/galaxy/tools/deps/mulled/mulled_build_tool.py
M lib/galaxy/tools/deps/mulled/util.py
M lib/galaxy/tools/deps/resolvers/__init__.py
M lib/galaxy/tools/deps/resolvers/conda.py
M lib/galaxy/tools/deps/resolvers/galaxy_packages.py
M lib/galaxy/tools/error_reports/plugins/biostars.py
M lib/galaxy/tools/error_reports/plugins/email.py
M lib/galaxy/tools/error_reports/plugins/github.py
M lib/galaxy/tools/error_reports/plugins/influxdb.py
M lib/galaxy/tools/error_reports/plugins/json.py
M lib/galaxy/tools/error_reports/plugins/sentry.py
M lib/galaxy/tools/imp_exp/__init__.py
M lib/galaxy/tools/lint.py
M lib/galaxy/tools/linters/inputs.py
M lib/galaxy/tools/locations/__init__.py
M lib/galaxy/tools/locations/dockstore.py
M lib/galaxy/tools/locations/http.py
M lib/galaxy/tools/parameters/__init__.py
M lib/galaxy/tools/parameters/basic.py
M lib/galaxy/tools/parameters/dynamic_options.py
M lib/galaxy/tools/parameters/output_collect.py
M lib/galaxy/tools/parser/cwl.py
M lib/galaxy/tools/parser/factory.py
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/parser/yaml.py
M lib/galaxy/tools/toolbox/__init__.py
M lib/galaxy/tools/toolbox/base.py
M lib/galaxy/tools/toolbox/filters/__init__.py
M lib/galaxy/tools/toolbox/lineages/factory.py
M lib/galaxy/tools/toolbox/lineages/interface.py
M lib/galaxy/tools/toolbox/panel.py
M lib/galaxy/tools/toolbox/watcher.py
M lib/galaxy/tools/verify/__init__.py
M lib/galaxy/tools/verify/test_data.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/tours/__init__.py
M lib/galaxy/util/__init__.py
M lib/galaxy/util/biostar.py
M lib/galaxy/util/hash_util.py
M lib/galaxy/util/object_wrapper.py
M lib/galaxy/util/pastescript/loadwsgi.py
M lib/galaxy/util/submodules.py
M lib/galaxy/util/xml_macros.py
M lib/galaxy/visualization/data_providers/genome.py
M lib/galaxy/visualization/data_providers/phyloviz/__init__.py
M lib/galaxy/visualization/data_providers/phyloviz/newickparser.py
M lib/galaxy/visualization/data_providers/phyloviz/nexusparser.py
M lib/galaxy/visualization/data_providers/phyloviz/phyloxmlparser.py
M lib/galaxy/visualization/data_providers/registry.py
M lib/galaxy/visualization/plugins/config_parser.py
M lib/galaxy/visualization/plugins/registry.py
M lib/galaxy/visualization/plugins/resource_parser.py
M lib/galaxy/web/form_builder.py
M lib/galaxy/web/framework/formbuilder.py
M lib/galaxy/web/framework/helpers/__init__.py
M lib/galaxy/web/framework/middleware/batch.py
M lib/galaxy/web/framework/middleware/graphite.py
M lib/galaxy/web/framework/middleware/profile.py
M lib/galaxy/web/framework/middleware/remoteuser.py
M lib/galaxy/web/framework/openid_manager.py
M lib/galaxy/web/proxy/__init__.py
M lib/galaxy/web/security/__init__.py
M lib/galaxy/webapps/config_manage.py
M lib/galaxy/webapps/galaxy/api/annotations.py
M lib/galaxy/webapps/galaxy/api/configuration.py
M lib/galaxy/webapps/galaxy/api/dataset_collections.py
M lib/galaxy/webapps/galaxy/api/datasets.py
M lib/galaxy/webapps/galaxy/api/datatypes.py
M lib/galaxy/webapps/galaxy/api/extended_metadata.py
M lib/galaxy/webapps/galaxy/api/folder_contents.py
M lib/galaxy/webapps/galaxy/api/folders.py
M lib/galaxy/webapps/galaxy/api/forms.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
M lib/galaxy/webapps/galaxy/api/item_tags.py
M lib/galaxy/webapps/galaxy/api/job_files.py
M lib/galaxy/webapps/galaxy/api/jobs.py
M lib/galaxy/webapps/galaxy/api/libraries.py
M lib/galaxy/webapps/galaxy/api/library_contents.py
M lib/galaxy/webapps/galaxy/api/library_datasets.py
M lib/galaxy/webapps/galaxy/api/metrics.py
M lib/galaxy/webapps/galaxy/api/page_revisions.py
M lib/galaxy/webapps/galaxy/api/pages.py
M lib/galaxy/webapps/galaxy/api/provenance.py
M lib/galaxy/webapps/galaxy/api/quotas.py
M lib/galaxy/webapps/galaxy/api/remote_files.py
M lib/galaxy/webapps/galaxy/api/search.py
M lib/galaxy/webapps/galaxy/api/tool_dependencies.py
M lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py
M lib/galaxy/webapps/galaxy/api/toolshed.py
M lib/galaxy/webapps/galaxy/api/visualizations.py
M lib/galaxy/webapps/galaxy/api/webhooks.py
M lib/galaxy/webapps/galaxy/api/workflows.py
M lib/galaxy/webapps/galaxy/controllers/admin.py
M lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
M lib/galaxy/webapps/galaxy/controllers/biostar.py
M lib/galaxy/webapps/galaxy/controllers/library.py
R lib/galaxy/webapps/galaxy/controllers/library_admin.py
R lib/galaxy/webapps/galaxy/controllers/library_common.py
M lib/galaxy/webapps/galaxy/controllers/tag.py
M lib/galaxy/webapps/galaxy/controllers/user.py
M lib/galaxy/webapps/galaxy/controllers/visualization.py
M lib/galaxy/webapps/galaxy/controllers/workflow.py
M lib/galaxy/webapps/reports/app.py
M lib/galaxy/webapps/reports/controllers/history.py
M lib/galaxy/webapps/reports/controllers/home.py
M lib/galaxy/webapps/reports/controllers/jobs.py
M lib/galaxy/webapps/reports/controllers/root.py
M lib/galaxy/webapps/reports/controllers/sample_tracking.py
M lib/galaxy/webapps/reports/controllers/users.py
M lib/galaxy/webapps/reports/controllers/workflows.py
M lib/galaxy/webapps/tool_shed/api/authenticate.py
M lib/galaxy/webapps/tool_shed/api/categories.py
M lib/galaxy/webapps/tool_shed/api/configuration.py
M lib/galaxy/webapps/tool_shed/api/groups.py
M lib/galaxy/webapps/tool_shed/api/repositories.py
M lib/galaxy/webapps/tool_shed/api/tools.py
M lib/galaxy/webapps/tool_shed/api/users.py
M lib/galaxy/webapps/tool_shed/app.py
M lib/galaxy/webapps/tool_shed/controllers/admin.py
M lib/galaxy/webapps/tool_shed/controllers/repository_review.py
M lib/galaxy/webapps/tool_shed/controllers/upload.py
M lib/galaxy/webapps/tool_shed/controllers/user.py
M lib/galaxy/webapps/tool_shed/search/tool_search.py
M lib/galaxy/webapps/tool_shed/util/hgweb_config.py
M lib/galaxy/workflow/extract.py
M lib/galaxy/workflow/schedulers/core.py
M lib/tool_shed/capsule/capsule_manager.py
M lib/tool_shed/dependencies/attribute_handlers.py
M lib/tool_shed/galaxy_install/install_manager.py
M lib/tool_shed/galaxy_install/tool_dependencies/recipe/install_environment.py
M lib/tool_shed/galaxy_install/tool_migration_manager.py
M lib/tool_shed/galaxy_install/tools/tool_panel_manager.py
M lib/tool_shed/repository_types/registry.py
M lib/tool_shed/tools/data_table_manager.py
M lib/tool_shed/tools/tool_validator.py
M lib/tool_shed/tools/tool_version_manager.py
M lib/tool_shed/util/hg_util.py
M lib/tool_shed/util/shed_util_common.py
M lib/tool_shed/util/tool_util.py
M lib/tool_shed/utility_containers/__init__.py
M run_tests.sh
M scripts/common_startup.sh
M scripts/functional_tests.py
M scripts/manage_tool_dependencies.py
M static/maps/mvc/collection/collection-model.js.map
M static/maps/mvc/collection/collection-view.js.map
M static/maps/mvc/history/hda-li.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
A static/maps/mvc/history/history-item-li.js.map
M static/maps/mvc/history/history-model.js.map
M static/maps/mvc/history/history-view.js.map
M static/maps/mvc/tool/tool-form-base.js.map
M static/maps/utils/ajax-queue.js.map
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/mvc/collection/collection-model.js
M static/scripts/mvc/collection/collection-view.js
M static/scripts/mvc/history/hda-li.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
A static/scripts/mvc/history/history-item-li.js
M static/scripts/mvc/history/history-model.js
M static/scripts/mvc/history/history-view.js
M static/scripts/mvc/tool/tool-form-base.js
M static/scripts/utils/ajax-queue.js
R templates/admin/library/grid.mako
R templates/admin/library/new_library.mako
M templates/admin/tool_shed_repository/repository_actions_menu.mako
M templates/admin/tool_shed_repository/view_tool_metadata.mako
R templates/search/index.mako
M templates/show_params.mako
M templates/webapps/galaxy/admin/center.mako
R templates/webapps/galaxy/library/common/browse_library.mako
R templates/webapps/galaxy/library/common/browse_library_opt.mako
R templates/webapps/galaxy/library/common/common.mako
R templates/webapps/galaxy/library/common/folder_info.mako
R templates/webapps/galaxy/library/common/folder_permissions.mako
R templates/webapps/galaxy/library/common/import_datasets_to_histories.mako
R templates/webapps/galaxy/library/common/ldda_edit_info.mako
R templates/webapps/galaxy/library/common/ldda_info.mako
R templates/webapps/galaxy/library/common/ldda_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_info.mako
R templates/webapps/galaxy/library/common/library_dataset_permissions.mako
R templates/webapps/galaxy/library/common/library_dataset_search_results.mako
R templates/webapps/galaxy/library/common/library_info.mako
R templates/webapps/galaxy/library/common/library_item_info.mako
R templates/webapps/galaxy/library/common/library_permissions.mako
R templates/webapps/galaxy/library/common/move_library_item.mako
R templates/webapps/galaxy/library/common/new_folder.mako
R templates/webapps/galaxy/library/common/upload.mako
R templates/webapps/galaxy/library/grid.mako
R templates/webapps/galaxy/library/index.mako
M test/api/test_jobs.py
M test/api/test_page_revisions.py
M test/base/driver_util.py
M test/base/populators.py
M test/base/testcase.py
M test/functional/test_toolbox.py
A test/functional/tools/cat_data_and_sleep.xml
M test/functional/tools/samples_tool_conf.xml
A test/functional/webhooks/tour_generator
M test/galaxy_selenium/components.py
M test/galaxy_selenium/data.py
M test/galaxy_selenium/navigates_galaxy.py
M test/galaxy_selenium/navigation.yml
A test/integration/test_local_job_cancellation.py
M test/manual/workflows_scaling.py
M test/selenium_tests/framework.py
M test/selenium_tests/test_collection_builders.py
M test/selenium_tests/test_history_dataset_state.py
M test/selenium_tests/test_history_sharing.py
M test/selenium_tests/test_jupyter.py
M test/selenium_tests/test_library_contents.py
M test/selenium_tests/test_library_landing.py
M test/selenium_tests/test_published_histories_grid.py
M test/selenium_tests/test_saved_histories.py
M test/selenium_tests/test_stock_tours.py
A test/selenium_tests/test_tool_describing_tours.py
M test/selenium_tests/test_tool_form.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/twilltestcase.py
M test/unit/datatypes/dataproviders/test_base_dataproviders.py
M test/unit/datatypes/dataproviders/test_line_dataproviders.py
M test/unit/jobs/dynamic_tool_destination/test_dynamic_tool_destination.py
M test/unit/jobs/test_job_wrapper.py
M test/unit/jobs/test_mapper.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_DatasetManager.py
M test/unit/managers/test_HDAManager.py
M test/unit/managers/test_HDCAManager.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_objectstore.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_parsing.py
M test/unit/tools/test_select_parameters.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_watcher.py
M test/unit/tools_support.py
M test/unit/visualizations/plugins/test_VisualizationPlugin.py
M test/unit/visualizations/plugins/test_VisualizationsRegistry.py
M test/unit/web/framework/test_webapp.py
M test/unit/workflows/test_modules.py
M test/unit/workflows/test_run_parameters.py
M test/unit/workflows/test_workflow_progress.py
M tools/filters/gff/gff_filter_by_attribute.py
M tools/filters/gff/gff_filter_by_feature_count.py
M tools/phenotype_association/senatag.py
M tox.ini
Log Message:
-----------
Merge remote-tracking branch 'origin/dev' into job-handler-mules
Commit: e68b8a312e3051b9378e59340ef42dd91302c1c0
https://github.com/galaxyproject/galaxy/commit/e68b8a312e3051b9378e59340ef4…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-15 (Wed, 15 Nov 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/util/facts.py
Log Message:
-----------
Fix use of configure_logging() by scripts that pass the config as a dict
rather than a galaxy configuration object
Commit: c270614fac007c35eefe473a9023964d7feafe89
https://github.com/galaxyproject/galaxy/commit/c270614fac007c35eefe473a9023…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-16 (Thu, 16 Nov 2017)
Changed paths:
M lib/galaxy/tools/parser/xml.py
M lib/galaxy/tools/xsd/galaxy.xsd
M lib/galaxy/webapps/galaxy/api/history_contents.py
M templates/user/register.mako
M test/api/test_history_contents.py
M test/api/test_libraries.py
M test/api/test_workflows.py
M test/base/populators.py
M test/functional/tools/create_2.xml
M test/integration/test_data_manager_table_reload.py
M tools/data_source/microbial_import.xml
Log Message:
-----------
Merge remote-tracking branch 'origin/dev' into job-handler-mules
Commit: 43138be11f8194dabc4645d20d58bb156f9bdb3c
https://github.com/galaxyproject/galaxy/commit/43138be11f8194dabc4645d20d58…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-16 (Thu, 16 Nov 2017)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Reenable automatic silencing of chatty loggers by default. This is
needed when Paste is used but PasteDeploy is not, e.g. with tests.
Commit: f78436bba0209d5d886387f81020d3383e08c327
https://github.com/galaxyproject/galaxy/commit/f78436bba0209d5d886387f81020…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-17 (Fri, 17 Nov 2017)
Changed paths:
M lib/galaxy/util/facts.py
Log Message:
-----------
Fix None server_name when using the default under uWSGI
Commit: c18521d7f774febb75a715e4de7926ff957daab9
https://github.com/galaxyproject/galaxy/commit/c18521d7f774febb75a715e4de79…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-17 (Fri, 17 Nov 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/web/stack/__init__.py
M scripts/galaxy-main
Log Message:
-----------
Move signal handling from uWSGI stack to main
Commit: 1ec960bcf66769c682135901cbd4623b6719fdf8
https://github.com/galaxyproject/galaxy/commit/1ec960bcf66769c682135901cbd4…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-17 (Fri, 17 Nov 2017)
Changed paths:
M lib/galaxy/web/stack/__init__.py
M lib/galaxy/web/stack/message.py
M lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/galaxy/buildapp.py
M scripts/galaxy-main
M scripts/get_uwsgi_args.py
Log Message:
-----------
Improve shutdown cleanliness under uWSGI.
Commit: b4863b2df8214972b5e14b0b318591e1ded613f6
https://github.com/galaxyproject/galaxy/commit/b4863b2df8214972b5e14b0b3185…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-17 (Fri, 17 Nov 2017)
Changed paths:
M lib/galaxy/app.py
M scripts/galaxy-main
Log Message:
-----------
Fix lint errors
Commit: eda29c81c16c4422167c7d22f7a79980f7799baa
https://github.com/galaxyproject/galaxy/commit/eda29c81c16c4422167c7d22f7a7…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-17 (Fri, 17 Nov 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/webapps/tool_shed/config.py
M test/base/driver_util.py
M test/shed_functional/functional_tests.py
Log Message:
-----------
Remove deprecated job runner URL config options
Commit: e858ceb84a340c658c682d33e350eb7c19649978
https://github.com/galaxyproject/galaxy/commit/e858ceb84a340c658c682d33e350…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-17 (Fri, 17 Nov 2017)
Changed paths:
M config/galaxy.ini.sample
M scripts/get_uwsgi_args.py
Log Message:
-----------
Do not autostart uWSGI mules
Commit: 47473cb85d38a4c7c4ccc9c03186787693f28efb
https://github.com/galaxyproject/galaxy/commit/47473cb85d38a4c7c4ccc9c03186…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-17 (Fri, 17 Nov 2017)
Changed paths:
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Postfork thread start fixes
Commit: e8a22447fd6b9d5f077e2d6b8a0d1144b2cb20db
https://github.com/galaxyproject/galaxy/commit/e8a22447fd6b9d5f077e2d6b8a0d…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-17 (Fri, 17 Nov 2017)
Changed paths:
M lib/galaxy/util/handlers.py
Log Message:
-----------
Run jobs in web workers if no job-handlers farm is configured and using
a default job conf (no job_conf.xml)
Commit: 49158ba38ba7204a078f2da22ddd6bad75c25f23
https://github.com/galaxyproject/galaxy/commit/49158ba38ba7204a078f2da22ddd…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-17 (Fri, 17 Nov 2017)
Changed paths:
M lib/galaxy/web/stack/__init__.py
M scripts/galaxy-main
Log Message:
-----------
Add multi-farm support to the main script
Commit: 2764fe0b5cb73087f76c701a6faf1e71b3c96394
https://github.com/galaxyproject/galaxy/commit/2764fe0b5cb73087f76c701a6faf…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/util/facts.py
M lib/galaxy/web/stack/__init__.py
Log Message:
-----------
Fix/improve server name manipulation
Commit: 4b2c177ae504af7d290d1a6ed436ce0ed4207400
https://github.com/galaxyproject/galaxy/commit/4b2c177ae504af7d290d1a6ed436…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths:
M lib/galaxy/app.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/util/handlers.py
M lib/galaxy/workflow/scheduling_manager.py
Log Message:
-----------
Attempt to deal with job_conf.xml handlers in a backwards-compatible
way.
Commit: a3346e2fb7c8cc4d800684f36bb3ca5ae82ced72
https://github.com/galaxyproject/galaxy/commit/a3346e2fb7c8cc4d800684f36bb3…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2017-11-20 (Mon, 20 Nov 2017)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Fix unit tests
Commit: c6c55e1046a74686d58f5de8010b6654b70e2421
https://github.com/galaxyproject/galaxy/commit/c6c55e1046a74686d58f5de8010b…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-28 (Tue, 28 Nov 2017)
Changed paths:
M config/workflow_schedulers_conf.xml.sample
M lib/galaxy/app.py
M lib/galaxy/config.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/handler.py
M lib/galaxy/jobs/manager.py
M lib/galaxy/jobs/runners/__init__.py
M lib/galaxy/model/orm/scripts.py
M lib/galaxy/tools/actions/__init__.py
M lib/galaxy/tools/actions/history_imp_exp.py
M lib/galaxy/tools/actions/metadata.py
M lib/galaxy/tools/actions/model_operations.py
M lib/galaxy/tools/actions/upload_common.py
A lib/galaxy/util/facts.py
M lib/galaxy/util/handlers.py
M lib/galaxy/util/path/__init__.py
M lib/galaxy/util/properties.py
M lib/galaxy/web/framework/webapp.py
M lib/galaxy/web/stack/__init__.py
A lib/galaxy/web/stack/message.py
A lib/galaxy/web/stack/transport.py
M lib/galaxy/webapps/galaxy/buildapp.py
M lib/galaxy/webapps/tool_shed/config.py
M lib/galaxy/workflow/scheduling_manager.py
M lib/tool_shed/galaxy_install/migrate/check.py
M lib/tool_shed/util/commit_util.py
R manage_tools.sh
M run.sh
M run_reports.sh
M run_tool_shed.sh
M scripts/common_startup_functions.sh
M scripts/galaxy-main
A scripts/get_uwsgi_args.py
R scripts/manage_tools.py
M test/base/driver_util.py
M test/base/integration_util.py
A test/functional/tools/config_vars.xml
M test/functional/tools/samples_tool_conf.xml
A test/integration/test_mules_as_job_handlers.py
M test/shed_functional/functional_tests.py
M test/unit/jobs/test_job_configuration.py
M test/unit/unittest_utils/galaxy_mock.py
Log Message:
-----------
Merge pull request #4475 from natefoo/job-handler-mules
Run Galaxy fully under uWSGI, including job handlers
Compare: https://github.com/galaxyproject/galaxy/compare/d82933d410f6...c6c55e1046a7
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: d868ffd08b8a5b539ba7977172e7c5a5c7be49a3
https://github.com/galaxyproject/galaxy/commit/d868ffd08b8a5b539ba7977172e7…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths:
M Makefile
A client/galaxy/scripts/qunit/test.js
M client/karma.config.js
M client/package.json
Log Message:
-----------
Improved qunit testing options.
- Speed up qunit testing but not re-building production bundles that aren't used anyway.
- Add a watch option for qunit.
- Add option to speed up running all tests by building tests as single bundle instead of many bundles. (May be future default for ``make client-test``.)
This is as close as I think we are going to get to closing #4843.
Commit: d82933d410f61fc703b5191d235f13f6b370a936
https://github.com/galaxyproject/galaxy/commit/d82933d410f61fc703b5191d235f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2017-11-26 (Sun, 26 Nov 2017)
Changed paths:
M Makefile
A client/galaxy/scripts/qunit/test.js
M client/karma.config.js
M client/package.json
Log Message:
-----------
Merge pull request #5066 from jmchilton/qunit_improvements
Improved Karma configuration and options.
Compare: https://github.com/galaxyproject/galaxy/compare/52eb970d1804...d82933d410f6
Branch: refs/heads/release_17.09
Home: https://github.com/galaxyproject/galaxy
Commit: cbc74f99e462ac3c71dc9bcb2a4c8c735e80170f
https://github.com/galaxyproject/galaxy/commit/cbc74f99e462ac3c71dc9bcb2a4c…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/integrated_panel.py
Log Message:
-----------
Ignore OSError when chmod'ing integrated_tool_panel_conf.xml
This fixes the first error in https://github.com/galaxyproject/galaxy/issues/5031:
```
Exception in thread ToolConfWatcher.thread:
Traceback (most recent call last):
File "/usr/lib/python2.7/threading.py", line 810, in __bootstrap_inner
self.run()
File "/usr/lib/python2.7/threading.py", line 763, in run
self.__target(*self.__args, **self.__kwargs)
File "lib/galaxy/tools/toolbox/watcher.py", line 138, in check
self.reload_callback()
File "lib/galaxy/webapps/galaxy/config_watchers.py", line 24, in <lambda>
self.tool_config_watcher = get_tool_conf_watcher(reload_callback=lambda: reload_toolbox(self.app), tool_cache=self.app.tool_cache)
File "lib/galaxy/queue_worker.py", line 92, in reload_toolbox
_get_new_toolbox(app)
File "lib/galaxy/queue_worker.py", line 111, in _get_new_toolbox
new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
File "lib/galaxy/tools/__init__.py", line 226, in __init__
app=app,
File "lib/galaxy/tools/toolbox/base.py", line 1061, in __init__
super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app)
File "lib/galaxy/tools/toolbox/base.py", line 87, in __init__
self._save_integrated_tool_panel()
File "lib/galaxy/tools/toolbox/integrated_panel.py", line 46, in _save_integrated_tool_panel
self._write_integrated_tool_panel_config_file()
File "lib/galaxy/tools/toolbox/integrated_panel.py", line 106, in _write_integrated_tool_panel_config_file
os.chmod(self._integrated_tool_panel_config, 0o644)
OSError: [Errno 2] No such file or directory: '/data/users/mvandenb/gx/config/integrated_tool_panel.xml'
```
Commit: a71d5aa2db41a289b9410b129e6e70652f456593
https://github.com/galaxyproject/galaxy/commit/a71d5aa2db41a289b9410b129e6e…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2017-11-24 (Fri, 24 Nov 2017)
Changed paths:
M lib/galaxy/tools/toolbox/integrated_panel.py
Log Message:
-----------
Merge pull request #5071 from mvdbeek/installation_fixes
[BUG][17.09] Ignore OSError when chmod'ing integrated_tool_panel_conf.xml
Compare: https://github.com/galaxyproject/galaxy/compare/a7c8edbaa448...a71d5aa2db41