Nicola Soranzo 975c8b605f Fix activation of `_galaxy_` conda env ...

- Use `conda_activate`, which works also under dash
- Run `conda_activate` also when `$GALAXY_CONDA_ENV` already exists
- Run `virtualenv` when the conda env is active but `$GALAXY_VIRTUAL_ENV`
  does not exist
- Update the default for `GALAXY_CONDA_ENV` in
  scripts/common_startup_functions.sh

Follow-up on https://github.com/galaxyproject/galaxy/pull/6975 .

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

..

api

Change all remaining old-style classes to new style

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

auth

Fixes for pycodestyle 2.2.0

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

cleanup_datasets

Lint

2018-10-15 16:07:14 -04:00

communication

Unification of Galaxy configuration parsing for scripts/*

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

grt

Change all remaining old-style classes to new style

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

loc_files

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

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

metagenomics

Python3: fix remaining print statements

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

microbes

Change all remaining old-style classes to new style

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

migrate_tools

Fix typos

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

slideshow

Fix many links

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

taxonomy

Tweaks to taxonomy tools

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

tool_shed

Fix errors reported by flake8 3.6.0

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

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

Change all remaining old-style classes to new style

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

bootstrap_history.py

Fix typos in `scripts/bootstrap_history.py`

2018-10-29 21:08:41 +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

Change all remaining old-style classes to new style

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

check_python.py

Fix errors reported by flake8 3.6.0

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

common_startup_functions.sh

Fix activation of `_galaxy_` conda env

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

common_startup.sh

Fix activation of `_galaxy_` conda env

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

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

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

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

Rework and simplify data manager testing

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

galaxy-main

Simplify importing from galaxy lib

2018-09-05 19:47:48 +01:00

get_platforms.py

Python3: fix remaining print statements

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

get_uwsgi_args.py

Add images to default static-safe location

2018-10-30 17:41:14 -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

pages_identifier_conversion.py

Skip the commit attempt, just flush on success

2018-09-07 13:20:34 -04:00

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

Fix symlinking during plugin staging

2018-09-19 11:16:54 +01:00

rst2html.py

Fix all E722 errors and ignore E741

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

runtime_stats.py

Fix errors reported by flake8 3.6.0

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

secret_decoder_ring.py

Prefer unicodify() for binary-to-text conversion

2018-08-21 12:35:05 +01:00

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

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