Nate Coraor 09feaf6f4d - 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

2017-09-01 01:08:16 -04:00

..

api

Fix E127 errors introduced by previous commit

2017-08-17 11:35:39 +01:00

auth

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

cleanup_datasets

Remove container config log message from cleanup scripts logs

2017-08-18 12:35:04 +01:00

communication

Fix import order and Python3 compatibility

2017-08-18 12:35:04 +01:00

data_libraries

Fix E127 errors introduced by previous commit

2017-08-17 11:35:39 +01:00

grt

not needed

2017-08-10 14:02:18 +02:00

loc_files

Fix E127 errors introduced by previous commit

2017-08-17 11:35:39 +01:00

metagenomics

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

microbes

Fix more indentation errors

2017-08-17 11:35:39 +01:00

migrate_tools

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

others

Fix E127 errors introduced by previous commit

2017-08-17 11:35:39 +01:00

slideshow

Align architecture slides with training-material remarkjs template.

2017-02-10 15:32:58 -05:00

taxonomy

Tweaks to taxonomy tools

2010-11-15 15:04:59 -05:00

tool_shed

Fix more indentation errors

2017-08-17 11:35:39 +01:00

tools

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

__init__.py

Adding db_shell.py that can be used to simplify writing command line

2012-03-05 12:11:53 -06:00

binary_compatibility.py

Add the scientific platform (Scientific Linux) as binary compatible

2016-02-03 13:33:42 -05:00

bootstrap_history.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

build_toolbox.py

Fix I201 errors from flake8-import-order

2016-11-23 18:31:04 +00:00

build_universe_config.py

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

check_eggs.py

Add stub fetch_eggs.py/check_eggs.py for people whose build/test/run

2015-11-06 11:06:11 -05:00

check_galaxy.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

check_python.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

common_startup_functions.sh

- Do all logging configuration other than paste fileConfig logging from

2017-09-01 01:08:16 -04:00

common_startup.sh

Pull build_sites out of datatypes conf.

2017-01-30 20:43:29 -05:00

config_sample_to_kwalify.py

Scripts to manage configuration infrastructure.

2017-08-10 13:14:55 -04:00

create_db.py

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

db_shell.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

drmaa_external_killer.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

drmaa_external_runner.py

Fix E127 errors introduced by previous commit

2017-08-17 11:35:39 +01:00

dump_tour.py

PEP-8 fix as pointed out by @nsoranzo.

2016-12-01 15:58:12 -05:00

edam_mapping.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

external_chown_script.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

extract_dataset_part.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

extract_toolbox_sections.py

Fix E127 errors introduced by previous commit

2017-08-17 11:35:39 +01:00

fetch_eggs.py

Python3: scripts/cleanup_datasets scripts/data_libraries

2016-06-25 21:49:25 -04:00

functional_tests.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

galaxy-main

- Do all logging configuration other than paste fileConfig logging from

2017-09-01 01:08:16 -04:00

get_platforms.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

get_uwsgi_args.py

- Do all logging configuration other than paste fileConfig logging from

2017-09-01 01:08:16 -04:00

helper.py

Fix E127 errors introduced by previous commit

2017-08-17 11:35:39 +01:00

manage_db.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

manage_tool_dependencies.py

Script reusage and generate uWSGI mule args

2017-08-21 21:36:48 -04:00

manage_tools.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

nosetests.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

paster.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

patch.sh

Add the script I used to create security patches

2016-02-24 16:54:30 -05:00

rst2html.py

Cleaning up modules. Still a few stragglers that can't be easily eggified.

2006-11-15 18:27:21 +00:00

runtime_stats.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

secret_decoder_ring.py

Fix import order and Python3 compatibility

2017-08-18 12:35:04 +01:00

set_dataset_sizes.py

Fix E127 errors introduced by previous commit

2017-08-17 11:35:39 +01:00

set_user_disk_usage.py

Fix E127 errors introduced by previous commit

2017-08-17 11:35:39 +01:00

summarize_timings.py

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

sync_reports_config.py

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +00:00

transfer.py

Fix E127 errors introduced by previous commit

2017-08-17 11:35:39 +01:00

update_shed_config_path.py

Fix all E201 and E202 style errors

2017-08-17 11:35:39 +01:00

validate_tools.sh

Refactor most of tool validation for CI into a standalone script.

2016-09-16 15:07:42 -04:00