Martin Cech fb449b4990 fix the logging init ...

- properly initialiaze the logger
- change level for some of the logs
- add some debug and critical logs

2018-07-09 15:53:49 -04:00

..

api

Replace unmaintained pycrypto dependency with pycryptodome

2018-06-13 03:07:04 +01:00

auth

Fixes for pycodestyle 2.2.0

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

cleanup_datasets

removed config.ini parameter from cleanup scripts

2018-04-23 14:58:48 +02:00

communication

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

grt

fix the logging init

2018-07-09 15:53:49 -04:00

loc_files

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +00:00

metagenomics

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

microbes

Stop shipping old BeautifulSoup library

2018-03-07 01:19:55 +00:00

migrate_tools

Fix typos

2018-03-05 09:44:26 +00:00

slideshow

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

taxonomy

Tweaks to taxonomy tools

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

tool_shed

Merge remote-tracking branch 'origin/dev' into ini_to_yaml_config

2018-01-18 12:30:05 -05:00

tools

Python3: fix remaining print statements

2017-10-12 18:34:29 +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

apply_tags.py

Add print statements with brackets

2018-03-09 08:01:56 +01:00

bootstrap_history.py

Add closing old milestone to release issue

2018-04-30 16:13:08 +01:00

build_toolbox.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

build_universe_config.py

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +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 E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

check_python.py

Allow Python 3 if in a virtualenv

2018-06-13 03:12:45 +01:00

common_startup_functions.sh

Merge branch 'release_18.01' into release_18.05

2018-06-06 15:58:08 +01:00

common_startup.sh

Call plugin static dir regeneration in the event client isn't being built (which also does this, albeit slightly differently)

2018-06-15 11:46:08 -04:00

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

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

docker_swarm_manager.py

Make the swarm manager recover on uncaught exceptions. It should do a

2018-04-13 12:34:55 -04:00

drmaa_external_killer.py

Fix all E201 and E202 style errors

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

drmaa_external_runner.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

dump_library_paths.py

Add a script for dumping library file paths for backup

2018-02-01 13:05:16 -05:00

dump_tour.py

Fix import order for cron/, scripts/ and test/

2017-09-25 23:44:39 +01:00

edam_mapping.py

Backport of hardening fixes to 17.09

2017-10-18 13:03:49 -04:00

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

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

fetch_eggs.py

Fix import order for cron/, scripts/ and test/

2017-09-25 23:44:39 +01:00

functional_tests.py

Enable conda_auto_init and conda_auto_install for framework tests

2018-01-17 17:11:41 +01:00

galaxy-main

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

get_platforms.py

Python3: fix remaining print statements

2017-10-12 18:34:29 +01:00

get_uwsgi_args.py

Add static-safe mapping for uwsgi for plugin static dirs, which are accessible via symlink

2018-06-15 14:11:19 -04:00

helper.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

maintenance.sh

Use consistent preference order for config files

2018-06-02 03:28:54 +01:00

manage_db.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

manage_tool_dependencies.py

To avoid duplication, move common utilities used by external scripts to

2017-11-13 12:18:09 -05:00

nosetests.py

Fix all E201 and E202 style errors

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

paster.py

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +00:00

patch.sh

Add the script I used to create security patches

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

plugin_staging.py

Use os.pardir instead of ../. Thanks @nsoranzo

2018-06-15 14:49:46 -04:00

rst2html.py

Fix all E722 errors and ignore E741

2017-10-24 11:29:09 +01:00

runtime_stats.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

secret_decoder_ring.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

set_dataset_sizes.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

set_user_disk_usage.py

Unification of Galaxy configuration parsing for scripts/*

2018-03-23 16:14:49 -04:00

summarize_timings.py

paster.pid/log to galaxy.pid/log reference update

2017-12-15 15:34:47 +00:00

sync_reports_config.py

Mark scripts/* that don't work with YAML configuraiton options as deprecated.

2018-03-23 16:14:49 -04:00

transfer.py

Mark scripts/* that don't work with YAML configuraiton options as deprecated.

2018-03-23 16:14:49 -04:00

update_shed_config_path.py

Python3: finish first pass on whole codebase

2017-12-14 12:01:01 +00:00

validate_tools.sh

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

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