Martin Cech e45d7959a7 Merge pull request #8308 from jmchilton/push_scripts_into_subpackages ...

Push galaxy-meta scripts into appropiate subpackages.

2019-07-15 18:45:13 -04:00

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api

Use `yaml.safe_load() instead of load()`

2019-04-23 16:50:55 +01:00

auth

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cleanup_datasets

Fix issues reported by ShellCheck

2019-06-13 12:53:26 +01:00

communication

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -04:00

grt

swap to exception

2019-04-26 13:29:12 +02:00

loc_files

Replace deprecated xml.etree.ElementTree.Element.getiterator() with iter()

2018-09-18 10:06:13 +01:00

metagenomics

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microbes

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

slideshow

Fix many links

2018-09-03 14:34:13 +01:00

taxonomy

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tool_shed

Update import paths for loader_directory

2019-07-06 00:52:45 +02:00

tools

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__init__.py

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apply_tags.py

Change all remaining old-style classes to new style

2018-09-17 12:26:07 +01:00

bootstrap_history.py

Fixes and enhancements for release note generation.

2019-05-24 16:59:32 -04:00

build_toolbox.py

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check_eggs.py

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check_python.py

Drop support for Python 3.4. Officially support Python >=3.5

2019-01-31 23:31:44 +00:00

common_startup_functions.sh

Fix activation of `_galaxy_` conda env

2018-12-14 00:22:12 +00:00

common_startup.sh

Merge pull request #8290 from natefoo/remove-ci-pip-progress-bar

2019-07-09 12:17:49 +02:00

config_sample_to_kwalify.py

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create_db.py

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db_shell.py

Fix traceback in `printquery()`

2019-06-11 11:31:40 +01:00

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

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drmaa_external_runner.py

external_runner: load json template first

2018-11-09 17:48:36 +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

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edam_mapping.py

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external_chown_script.py

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extract_dataset_part.py

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extract_toolbox_sections.py

Fix deprecated `getchildren()`

2019-04-23 12:51:13 +01:00

fetch_eggs.py

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functional_tests.py

Rework and simplify data manager testing

2018-08-13 17:19:25 +02:00

galaxy

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galaxy-main

Fix galaxy-main running from source now that setup,py is no longer in the root

2019-07-07 18:23:49 +02:00

get_platforms.py

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get_uwsgi_args.py

Drop static-safe navigation to plugin dirs. These are no longer symlinks, they are staged files.

2019-03-14 13:23:45 -04:00

helper.py

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -04:00

maintenance.sh

Fix issues reported by ShellCheck

2019-06-13 12:53:26 +01:00

manage_db.py

Unification of Galaxy configuration parsing for scripts/*

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

manage_tool_dependencies.py

Rework config locating logic (it was reading the sample again).

2019-07-08 11:28:31 +02:00

nosetests.py

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pages_identifier_conversion.py

clean-fix-page-api - move page revision creation to manager.

2019-05-29 13:43:49 -04:00

paster.py

Remove log_tempfile.

2019-07-08 14:52:13 +02:00

patch.sh

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plugin_staging.py

Update plugin_staging to actually stage instead of symlink, since it no longer needs to be quite as fast (on startup). This will allow us to drop unnecessary trust rules from uwsgi static.

2019-03-14 13:18:43 -04:00

rst2html.py

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runtime_stats.py

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +01:00

secret_decoder_ring.py

Refactor galaxy.web.security into galaxy.security.idencoding.

2019-03-19 14:28:31 -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

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +01:00

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

Fix errors reported by flake8 3.6.0

2018-10-24 23:22:19 +01:00

update_shed_config_path.py

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validate_tools.sh

Fix issues reported by ShellCheck

2019-06-13 12:53:26 +01:00