John Davis 889a8445bd Change parsing of --galaxy-config option ...

Rationale: alternate config file applies to all subcommands, so, I
think, it is more correct to run this:

> ./db.sh -c mygalaxy.yml upgrade some-revision-id

than this:

> ./db.sh upgrade some-revision-id -c mygalaxy.yml

That's also consistent with how alembic handles this option.

2022-09-28 15:24:49 -04:00

..

api

Drop more mappings that don't exist anymore

2022-03-21 13:14:43 +01:00

auth

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2022-02-03 07:42:20 -05:00

cleanup_datasets

s/eagerload/joinedload (SQLAlchemy 2.0)

2022-03-16 16:48:33 -04:00

grt

Merge branch 'release_22.01' into dev

2022-03-02 20:08:55 +00:00

loc_files

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metagenomics

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microbes

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objectstore

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slideshow

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2022-02-03 07:42:20 -05:00

taxonomy

Tweaks to taxonomy tools

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

tool_shed

Merge pull request #13562 from ic4f/dev_sa20_3

2022-03-20 18:37:17 -04:00

tools

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2022-02-03 07:42:20 -05:00

__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

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2022-02-03 07:42:20 -05:00

bootstrap_history.py

Update a couple PR titles, strip trailing . from PR titles

2022-08-19 12:29:25 +02:00

build_toolbox.py

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2022-02-03 07:42:20 -05:00

celery_shell.py

Fix a typo in celery_shell.py

2022-05-25 19:46:47 +02:00

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_model.py

Update db index testing: test both models, gxy and tsi

2022-03-09 18:41:03 -05:00

check_python.py

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2022-02-03 07:42:20 -05:00

common_startup_functions.sh

Fix first startup when only python3 is on PATH

2022-08-08 16:28:26 +02:00

common_startup.sh

Fix first startup when only python3 is on PATH

2022-08-08 16:28:26 +02:00

config_parse.py

Use `load_app_properties()` to load Galaxy config file

2022-04-26 09:48:18 +01:00

config_sample_to_kwalify.py

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2022-02-03 07:42:20 -05:00

create_db.py

Add create/migrate scripts for Alembic dbs (squashed)

2022-03-09 18:41:02 -05:00

create_toolshed_db.py

Apply black, isort (squashed)

2022-03-09 18:41:49 -05:00

cwl_conformance_to_test_cases.py

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2022-02-03 07:42:20 -05:00

db_shell.py

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2022-02-03 07:42:20 -05:00

db.py

Change parsing of --galaxy-config option

2022-09-28 15:24:49 -04:00

drmaa_external_killer.py

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drmaa_external_runner.py

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dump_library_paths.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

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fetch_eggs.py

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fix_dm_versions.py

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2022-02-03 07:42:20 -05:00

functional_tests.py

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2022-02-03 07:42:20 -05:00

galaxy_main.py

First pass in dropping uwsgi specific things

2022-03-15 21:31:59 +01:00

galaxy_schemadisp.py

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2022-02-03 07:42:20 -05:00

galaxy-main

Adjust galaxy-main script so we can import from it for easy app setup

2020-12-22 11:18:00 +01:00

helper.py

Merge branch 'release_22.01' into dev

2022-03-02 20:08:55 +00:00

maintenance.sh

Fix issues reported by ShellCheck

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

manage_db_adapter.py

Verify db initialization before running upgrade script

2022-07-13 16:38:11 -04:00

manage_db.py

Update inline documentation in scripts

2022-05-31 10:30:30 -04:00

manage_tool_dependencies.py

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2022-02-03 07:42:20 -05:00

migrate_db.py

Adapt manage_db.py for usegalaxy playbook; add tests

2022-03-09 18:41:50 -05:00

migrate_toolshed_db.py

Apply black, isort (squashed)

2022-03-09 18:41:49 -05:00

pages_identifier_conversion.py

Merge branch 'release_22.01' into dev

2022-03-02 20:08:55 +00:00

patch.sh

Add the script I used to create security patches

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

plugin_staging.py

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2022-02-03 07:42:20 -05:00

release-diff.py

Write admin announce, add deferred datasets to user announcement

2022-08-19 16:11:41 +02:00

release.sh

Update release.sh script for new packaging layout

2022-08-23 16:04:24 +02:00

resumable_upload.py

Merge branch 'release_22.01' into release_22.05

2022-07-02 18:07:38 +02:00

rst2html.py

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2022-02-03 07:42:20 -05:00

runtime_stats.py

Upgrade syntax to Python 3.7

2022-03-14 14:57:43 +00:00

secret_decoder_ring.py

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2022-02-03 07:42:20 -05:00

set_dataset_sizes.py

Merge branch 'release_22.01' into dev

2022-03-02 20:08:55 +00:00

set_user_disk_usage.py

Merge branch 'release_22.01' into dev

2022-03-02 20:08:55 +00:00

summarize_timings.py

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tests_markdown_compare.tpl

Performance metrics for tests.

2021-02-12 20:44:05 -05:00

tests_markdown.py

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tests_markdown.tpl

Performance metrics for tests.

2021-02-12 20:44:05 -05:00

update_cwl_conformance_tests.sh

Add CWL conformance API tests

2021-11-23 14:10:21 +00:00

update_shed_config_path.py

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2022-02-03 07:42:20 -05:00

validate_tools.sh

Switch to lxml for xml parsing

2020-05-12 15:00:27 +02:00

validate_tours.sh

Tour validation.

2022-06-02 14:53:55 -04:00