Nate Coraor 6c9d497e82 Only set $GALAXY_DAEMON_LOG when using gravity since other servers have ...

their own means of setting a log file. Read the supervisor log if it
exists and the daemon log does not, since failure to start Galaxy will
prevent creation of the daemon log file.

When running first startup in CI, attempt to read log files from
multiple places to make debugging different types of failures possible.

2022-01-26 14:50:39 -05:00

..

api

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

auth

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

cleanup_datasets

Drop old sqlalchemy patterns

2021-12-16 12:30:49 +01:00

grt

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

interactivetools

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

loc_files

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

metagenomics

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

microbes

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

objectstore

Remove unnecessary list creations

2021-11-29 16:33:05 +00:00

slideshow

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

taxonomy

…

tool_shed

Drop old sqlalchemy patterns

2021-12-16 12:30:49 +01:00

tools

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

__init__.py

…

apply_tags.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

bootstrap_history.py

Adjust check_blocking_issues to PyGithub usage

2021-11-01 13:01:02 +01:00

build_toolbox.py

Fix remaining issues reported by bugbear; add it to flake8 reqs

2021-01-16 05:58:15 +00:00

celery_shell.py

Add interactive shell for celery tasks

2021-11-29 10:34:01 +01:00

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

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

check_python.py

Drop support for Python 3.6, add Python 3.10

2021-12-08 08:14:10 +00:00

common_startup_functions.sh

Only set $GALAXY_DAEMON_LOG when using gravity since other servers have

2022-01-26 14:50:39 -05:00

common_startup.sh

If creating venv, modify activate to set $GRAVITY_STATE_DIR so that

2022-01-21 09:51:34 -05:00

config_sample_to_kwalify.py

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

create_db.py

Create install database with create_db.sh

2021-03-30 13:44:36 +02:00

cwl_conformance_to_test_cases.py

Remove unnecessary list creations

2021-11-29 16:33:05 +00:00

db_shell.py

Add interactive shell for celery tasks

2021-11-29 10:34:01 +01:00

docker_swarm_manager.py

New pyupgrade fixes

2021-10-24 12:10:34 +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

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

dump_library_paths.py

Add a script for dumping library file paths for backup

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

edam_mapping.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +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

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

extract_toolbox_sections.py

Fix all E203, E741 and W504 flake8 errors

2021-01-18 10:35:41 +00:00

fetch_eggs.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

fix_dm_versions.py

add script for fixing shed_data_manager_conf.xml

2021-07-14 17:13:26 +02:00

functional_tests.py

Cleanup galaxy_test.base.api_util.

2021-01-16 20:11:39 -05:00

galaxy

Make Galaxy installable the Pythonic way via setup.py. Incomplete, but

2016-07-07 13:49:27 -04:00

galaxy_main.py

First pass fstring conversion

2021-05-11 13:47:00 -04:00

galaxy_schemadisp.py

Lint fixes, prompt for sqlalchemy_schemadisplay install

2021-01-12 08:23:10 -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

get_platforms.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

get_uwsgi_args.py

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

helper.py

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

maintenance.sh

Fix issues reported by ShellCheck

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

manage_db.py

Enable on-screen logging for create_db.py and manage_db.py

2019-08-18 11:17:34 +01:00

manage_tool_dependencies.py

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

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

nosetests.py

Fix all E201 and E202 style errors

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

pages_identifier_conversion.py

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

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

paster.py

Restore pastescript, make new stack depend on APP_WEBSERVER=dev

2021-04-07 14:39:06 +02:00

patch.sh

Add the script I used to create security patches

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

plugin_staging.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

release-diff.py

Adjust release-diff.py

2022-01-19 18:20:19 +00:00

release.sh

Test Galaxy release script

2021-12-08 10:43:09 +00:00

resumable_upload.py

Adapt scripts/resumable_upload.py to fetch API

2021-10-13 18:05:42 +02:00

rst2html.py

Fix all E722 errors and ignore E741

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

runtime_stats.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +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

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

set_user_disk_usage.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

summarize_timings.py

Drop support for retired Python 3.5

2020-10-07 11:52:13 +01:00

tests_markdown_compare.tpl

Performance metrics for tests.

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

tests_markdown.py

New pyupgrade fixes

2021-10-24 12:10:34 +01:00

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

Don't use triple-quoted strings as comments

2021-11-29 23:02:34 +00:00

validate_tools.sh

Switch to lxml for xml parsing

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