John Chilton 2829a1f164 Merge pull request #5854 from natefoo/run-scripts-conda ...

Improve startup interoperability with Conda

2018-04-18 16:08:13 -04:00

..

api

Hierarchical upload API optimized for folders & collections.

2018-03-08 10:33:36 -05:00

auth

Fixes for pycodestyle 2.2.0

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

cleanup_datasets

Remove two scripts - dataset purging hasn't worked this way for a very long time.

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

communication

Unification of Galaxy configuration parsing for scripts/*

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

grt

More grt fixes - spotted by @nsoranzo.

2018-03-23 16:14:50 -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

Fix typo

2018-03-19 18:10:04 +00:00

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

Fix all E201 and E202 style errors

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

common_startup_functions.sh

Clean up and useability enhancements

2018-04-04 21:03:08 -04:00

common_startup_variables.sh

add maintenance.sh to simplify setting up a cleanup cron job or run the cleanup scripts in general

2017-11-02 11:06:26 +01:00

common_startup.sh

Look for both base and root conda envs

2018-04-04 23:18:57 -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

Don't set uWSGI's virtualenv option when running from Conda

2018-04-04 16:47:36 -04:00

helper.py

Unification of Galaxy configuration parsing for scripts/*

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

maintenance.sh

fix location of cleanup_datasets.py if executed outside of the root

2017-11-02 12:37:39 +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

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