John Chilton 3d9cdeb70c Outline infrastructure for managing Conda installations outside of Galaxy. ...

- Construct a DependencyManager according to Galaxy's configuration before Galaxy starts to allow auto installation of Conda.
- Add script for managing tool dependencies outside of a Galaxy environment.
- Refactor to allow this to be done without duplicating logic related to defaults, configuration handling, etc....

Implements #3426.

2017-01-23 09:47:18 -05:00

..

api

Fix I201 errors from flake8-import-order

2016-11-23 18:31:04 +00:00

auth

Fixes for pycodestyle 2.2.0

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

cleanup_datasets

Fix I201 errors from flake8-import-order

2016-11-23 18:31:04 +00:00

communication

Fixes for pycodestyle 2.2.0

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

data_libraries

Fixes for pycodestyle 2.2.0

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

loc_files

Fixes for pycodestyle 2.2.0

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

metagenomics

Partially lint scripts/ .

2015-07-13 20:13:28 +01:00

microbes

Fixes for pycodestyle 2.2.0

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

migrate_tools

Use __file__ when adding paths to sys.path instead of os.getcwd() .

2016-02-18 15:45:15 +00:00

others

Fixes for pycodestyle 2.2.0

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

slideshow

Fixes for pycodestyle 2.2.0

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

taxonomy

Tweaks to taxonomy tools

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

tool_shed

Fixes for pycodestyle 2.2.0

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

tools

Fixes for pycodestyle 2.2.0

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

__init__.py

Adding db_shell.py that can be used to simplify writing command line

2012-03-05 12:11:53 -06:00

binary_compatibility.py

Add the scientific platform (Scientific Linux) as binary compatible

2016-02-03 13:33:42 -05:00

bootstrap_history.py

Merge branch 'release_16.10' into dev

2016-12-07 20:35:40 +00:00

build_toolbox.py

Fix I201 errors from flake8-import-order

2016-11-23 18:31:04 +00:00

build_universe_config.py

Fixes for pycodestyle 2.2.0

2016-11-15 16:56:50 +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 I201 errors from flake8-import-order

2016-11-23 18:31:04 +00:00

check_python.py

Fix I201 errors from flake8-import-order

2016-11-23 18:31:04 +00:00

common_startup.sh

Slight clarification of run.sh messaging when using conda.

2016-11-16 16:16:33 -05:00

create_db.py

Fixes for pycodestyle 2.2.0

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

db_shell.py

Change remaining __all__ from list to tuple

2016-10-18 19:24:31 +01:00

drmaa_external_killer.py

Fixes for pycodestyle 2.2.0

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

drmaa_external_runner.py

Fix I201 errors from flake8-import-order

2016-11-23 18:31:04 +00:00

dump_tour.py

PEP-8 fix as pointed out by @nsoranzo.

2016-12-01 15:58:12 -05:00

edam_mapping.py

Use __file__ when adding paths to sys.path instead of os.getcwd() .

2016-02-18 15:45:15 +00:00

external_chown_script.py

Fixes for pycodestyle 2.2.0

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

extract_dataset_part.py

Fixes for pycodestyle 2.2.0

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

extract_toolbox_sections.py

Fixes for pycodestyle 2.2.0

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

fetch_eggs.py

Python3: scripts/cleanup_datasets scripts/data_libraries

2016-06-25 21:49:25 -04:00

functional_tests.py

Remove workflow testing stuff in test/functional and references.

2016-12-20 10:29:31 -05:00

galaxy-main

Fix a bunch of errors reported by Sphinx

2016-10-24 19:42:19 +01:00

get_platforms.py

Fix the remaining 1334 flake8 errors in scripts/ . Close #391.

2016-02-18 15:45:15 +00:00

grt.py

Fixes for pycodestyle 2.2.0

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

grt.yml.sample

grt.ini.sample is a YAML file, git it a YAML extension.

2016-07-21 14:31:25 -04:00

helper.py

Use __file__ when adding paths to sys.path instead of os.getcwd() .

2016-02-18 15:45:15 +00:00

manage_db.py

Fixes for pycodestyle 2.2.0

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

manage_tool_dependencies.py

Outline infrastructure for managing Conda installations outside of Galaxy.

2017-01-23 09:47:18 -05:00

manage_tools.py

Use __file__ when adding paths to sys.path instead of os.getcwd() .

2016-02-18 15:45:15 +00:00

nosetests.py

Fix unit tests exit status

2016-07-29 19:47:08 +01:00

paster.py

Use __file__ when adding paths to sys.path instead of os.getcwd() .

2016-02-18 15:45:15 +00:00

patch.sh

Add the script I used to create security patches

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

rst2html.py

Cleaning up modules. Still a few stragglers that can't be easily eggified.

2006-11-15 18:27:21 +00:00

runtime_stats.py

Fix more E203 flake8 errors

2016-05-17 23:53:16 +01:00

set_dataset_sizes.py

Fixes for pycodestyle 2.2.0

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

set_user_disk_usage.py

Fixes for pycodestyle 2.2.0

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

summarize_timings.py

Fixes for pycodestyle 2.2.0

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

sync_reports_config.py

Fixes for pycodestyle 2.2.0

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

transfer.py

Fixes for pycodestyle 2.2.0

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

update_shed_config_path.py

Fixes for pycodestyle 2.2.0

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

validate_tools.sh

Refactor most of tool validation for CI into a standalone script.

2016-09-16 15:07:42 -04:00