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bee9ebdbc126c15cd8a5eac4c6367e6398b8706e
Commit Graph
885 Commits
Author SHA1 Message Date
Nicola Soranzo 87d6239c36 Improve startup scripts 
Fix errors reported by shellcheck
 2016-08-11 15:28:28 +01:00
Dannon Baker 8c1be91231 Merge branch 'release_16.07' into dev 2016-08-09 07:44:58 -04:00
Ben 6516f20602 Update common_startup.sh to require python2.7 in .venv 
by changing the .venv creation to 'virtualenv -p python2.7' we force the python version we need.

The current suggestion on getgalaxy is: https://wiki.galaxyproject.org/Admin/Python
% mkdir ~/galaxy-python
% ln -s /path/to/python2.7 ~/galaxy-python/python
% export PATH=~/galaxy-python:$PATH

Which break lots of things, since we are working in a virtual environment anyway we can build it from the start with the version we want.

This will require that python 2.7 used in the virtual environment, and prevent breakage from multi-python deployed hosts. This simple change makes the software more accessible.

This edit built fine on OS X  10.10.5
python installed: 2.6, 2.7, 3.2, 3.5

galaxy.queue_worker INFO 2016-08-08 22:14:15,624 Binding and starting galaxy control worker for main
Starting server in PID 69210.
serving on http://127.0.0.1:8080
/Users/benc/Code/github/galaxy/.venv/lib/python2.7/site-packages/sqlalchemy/sql/sqltypes.py:565: SAWarning: Dialect sqlite+pysqlite does *not* support Decimal objects natively, and SQLAlchemy must convert from floating point - rounding errors and other issues may occur. Please consider storing Decimal numbers as strings or integers on this platform for lossless storage.
  'storage.' % (dialect.name, dialect.driver))
127.0.0.1 - - [08/Aug/2016:22:39:18 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/52.0.2743.116 Safari/537.36"
 2016-08-08 22:40:06 -04:00
Nicola Soranzo de3c50a5ef Python3 support and import order fixes for lib/tool_shed/ 2016-08-04 13:41:36 +01:00
Dannon Baker e291012afd Merge branch 'release_16.07' into dev 2016-07-29 15:35:29 -04:00
Nicola Soranzo 5e7f0c4b18 Fix unit tests exit status 
Broken in https://github.com/galaxyproject/galaxy/pull/2564
Also update scripts/nosetests.py
 2016-07-29 19:47:08 +01:00
Martin Cech 09aef7eda5 mention need to update P4's conf when freezing 2016-07-29 14:16:58 -04:00
Bjoern Gruening 6b8b0cde5b make client 2016-07-22 22:47:13 +02:00
John Chilton 8dbf987e10 Merge pull request #2455 from erasche/grt 
Galactic Radio Telescope
 2016-07-21 20:06:12 -04:00
John Chilton 76628c7203 Refactor grt.py method names to be clear public interface is only main(). 2016-07-21 14:59:29 -04:00
John Chilton bbe1d7bed0 Remove custom Galaxy config parsing in grt.py. 
Use existing abstractions - so things like environment variable based configuration will work.
 2016-07-21 14:59:29 -04:00
John Chilton 1f292824a1 Fix some obvious Python 2isms in grt client... 
... and one instance of bare exception.
 2016-07-21 14:59:27 -04:00
John Chilton a93874fe7b Define a main() function for grt client. 
This is purely stylistic - but I prefer to structure code to allow testing even if there are no actual test cases yet.

For more information see discussion here - http://stackoverflow.com/questions/4041238/why-use-def-main.
 2016-07-21 14:59:05 -04:00
John Chilton 6432eae251 Give grt a top-level docstring. 2016-07-21 14:33:58 -04:00
John Chilton 0280daebef grt.ini.sample is a YAML file, git it a YAML extension. 2016-07-21 14:31:25 -04:00
anuprulez 0d915ce131 Adding maximize/minimize feature to the communication channel 2016-07-14 14:11:44 +02:00
Dannon Baker 61a11341f9 When CONDA_ALREADY_INSTALLED is undefined there's an error due to the number of arguments in the boolean expression (we actually *do* always want a 1 or 0 there, never empty) 2016-07-08 10:52:08 -04:00
Remi Marenco de702db55d s/creation/activation. Thx @nsoranzo 2016-07-07 15:45:40 -04:00
remimarenco b53a9275d5 Add Warning when Conda is installed because we skip the virtualenv creation 
Fix the case where we could have conda not installed but not setting VirtualEnv still (and have this non relevant warning
 2016-07-07 14:34:40 -04:00
Dannon Baker a946b04316 Merge pull request #2574 from bxlab/python3 
Python3: port 215 files
 2016-07-05 09:57:54 -04:00
Eric Enns 417d43fb3e Added upload1 to tool blacklist 2016-06-26 09:19:57 -05:00
Nicola Soranzo cd13423953 Python3: small fixes to previous commits 2016-06-26 02:43:57 -04:00
Junzhou Wang f68a8198da Python3: scripts/cleanup_datasets scripts/data_libraries 2016-06-25 21:49:25 -04:00
Eric Enns 2fc3ffffff Removed unused copy import 2016-06-25 20:13:37 -05:00
Eric Enns 0383d47037 Added in params reporting with initial sanitization 2016-06-25 20:09:52 -05:00
Junzhou Wang e45f8abb54 Python3:script/api/ 2016-06-25 20:49:06 -04:00
Junzhou Wang a04f6589ea Python3: test/shed_functional/ and test/unit/ 2016-06-25 20:00:42 -04:00
Dannon Baker a0b20a61a2 Initialize objectstore for fix_set_dataset_sizes script (otherwise it doesn't currently run successfully) 2016-06-25 19:04:44 -04:00
Eric Enns 0c24b1c408 Fixed remaining flake8 issues 2016-06-25 14:26:40 -05:00
Eric Enns db4abace58 Flake8 fixes 2016-06-25 14:08:43 -05:00
Eric Enns 5cd9423677 Added grt_url to grt.ini.sample and removed default from argparse 2016-06-25 14:04:23 -05:00
Eric Enns c2239b1d9b Moved almost all cmd line parameters to config file. 2016-06-25 14:00:50 -05:00
Eric Enns 473b7eadc1 Added in tool_blacklist 2016-06-25 13:15:45 -05:00
Eric Enns bb3f026bfa Removed call to args.days 2016-06-25 13:00:22 -05:00
Eric Enns 722695a01b Added in last_job_id_sent and removed days options so no duplicates will be sent. 2016-06-25 12:54:19 -05:00
Eric Rasche d1d8642756 Change metric captured 2016-06-25 17:16:08 +00:00
Eric Rasche 012101692c Ignore metadata setting 2016-06-25 16:42:04 +00:00
Bjoern Gruening 1f1c35f708 merge 2016-06-19 21:49:15 +02:00
anuprulez 464e9a4261 Fixed issue with Firefox auto scrolling 2016-06-19 17:45:30 +02:00
anuprulez 008220d88d Adjusted the vertical position of gravatar icons 2016-06-19 15:47:09 +02:00
anuprulez feb00567e4 Adjusted the vertical position of gravatar icons 2016-06-19 15:44:20 +02:00
Bjoern Gruening 10c2764f09 add the identicon to gravatar 2016-06-19 13:21:26 +02:00
Bjoern Gruening e477d728d4 do not show gravatar for server messages 2016-06-19 10:30:45 +02:00
anuprulez c017b51666 Fixed UI issues and log deletion functionality in main tab 2016-06-19 02:29:20 +02:00
Bjoern Gruening b690abb46a make chat view a little bit more compact and fix bug in displaying "me" messages 2016-06-19 00:56:40 +02:00
Bjoern Gruening 4a304b63b1 fix pep8 2016-06-19 00:56:10 +02:00
Eric Rasche 83e61f1ca4 Support gravatar and rework template 2016-06-18 19:12:37 +00:00
anuprulez b8a92a3f80 Fixing issue with no persistent rooms 2016-06-18 17:20:38 +02:00
Bjoern Gruening 5ed647e34f release preparation 2016-06-18 10:33:03 +02:00
anuprulez 111a1c6222 Fixing the issue with persistent room names with spaces, adding fancy scroll bar, buttons instead of links for persistent rooms and UI changes for message area 2016-06-14 20:03:58 +02:00