John Chilton 08e2c351d9 Add edam formats to most Galaxy datatypes and a script for producing a mapping. ...

See notes in scripts/edam_mapping.py for more information on mapping.

This is based on mapping of terms done by Eric Rasche (@erasche) (in galaxyproject/galaxy#80) and by the team at Pasteur including @hmenager, @fmareuil, and @odoppelt (in https://docs.google.com/spreadsheets/d/1vptTpJvQfb5FOtRJOajjftUkL9aZ0eeVdhUPvd9h5wY/edit#gid=0).

Current mapping at time of commit is https://gist.github.com/jmchilton/73cd540d7a08488843d7.

2015-05-16 16:47:39 -04:00

..

api

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

cleanup_datasets

Uniform configuration of "From" field of sent emails.

2015-03-13 01:07:57 +00:00

data_libraries

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

loc_files

Convert everything from elementtree to stdlib xml module.

2015-01-29 16:10:56 -05:00

metagenomics

Switch to_json_string/from_json_string in galaxy/scripts.

2014-09-09 10:04:28 -04:00

microbes

Convert everything from elementtree to stdlib xml module.

2015-01-29 16:10:56 -05:00

migrate_tools

Migrate tools from the distribution to the tool shed.

2014-07-28 11:58:52 -04:00

others

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

scramble

Fix path insertion vs appending of <galaxy>/lib for all scripts.

2015-02-12 10:34:51 -05:00

taxonomy

Tweaks to taxonomy tools

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

tool_shed

found a known Whoosh bug, trying to avoid it

2015-01-29 11:43:29 -05:00

tools

Migrate 22 tools from the distribution to the tool shed.

2014-05-19 13:01:46 -04:00

__init__.py

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

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

build_toolbox.py

* Remove Todo's that have been done

2011-04-14 14:07:36 +02:00

build_universe_config.py

Fix merge() documentation.

2015-01-23 19:19:15 +00:00

check_eggs.py

Fix path insertion vs appending of <galaxy>/lib for all scripts.

2015-02-12 10:34:51 -05:00

check_galaxy.py

Fix path insertion vs appending of <galaxy>/lib for all scripts.

2015-02-12 10:34:51 -05:00

check_python.py

Require Python 2.6+ and remove various compatibility patches for 2.4 and 2.5

2013-04-09 11:57:38 -04:00

common_startup.sh

Ensure the correct default Galaxy config file is found in common_startup.sh, it

2015-02-12 11:47:58 -05:00

create_db.py

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

db_shell.py

Add utility for debugging sqlalchemy queries in db_shell.py.

2014-06-10 15:01:38 -05:00

dist-scramble.py

Fix path insertion vs appending of <galaxy>/lib for all scripts.

2015-02-12 10:34:51 -05:00

drmaa_external_killer.py

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

drmaa_external_runner.py

Fix for running LSF DRMAA jobs as 'real' user.

2014-08-18 08:43:37 -04:00

edam_mapping.py

Add edam formats to most Galaxy datatypes and a script for producing a mapping.

2015-05-16 16:47:39 -04:00

egg_packager_template.py

Fix the platform argument to fetch_eggs.py and create an egg packager for easing the installation/updating of Galaxy on systems without a direct connection to the internet.

2010-08-30 11:31:58 -04:00

external_chown_script.py

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

extract_dataset_part.py

Remove dependency on simplejson; convert everything over to using the json module in the python standard library.

2014-01-10 07:29:05 -05:00

extract_toolbox_sections.py

introduction of toolboxposition elements

2011-04-14 15:09:00 +02:00

fetch_eggs.py

Fix path manipulation during fetch_eggs. This getting an external version of pkg_resources (and not ours in lib/) is what is causing the weird egg fetching errors. Newer versions of pkg_resources create a mangled distribution string for some eggs with nonstandard version identifiers.

2015-02-12 08:28:37 -05:00

functional_tests.py

Dynamically fetch and cache test-data from git repositories if needed...

2015-02-09 21:43:42 -05:00

get_platforms.py

Fix path insertion vs appending of <galaxy>/lib for all scripts.

2015-02-12 10:34:51 -05:00

helper.py

Fix path insertion vs appending of <galaxy>/lib for all scripts.

2015-02-12 10:34:51 -05:00

make_egg_packager.py

Fix path insertion vs appending of <galaxy>/lib for all scripts.

2015-02-12 10:34:51 -05:00

manage_db.py

Add all the necessary dependency requires. Note to self: fix the egg dependency resolution bug so we don't have to dot his.

2015-02-14 10:35:42 -05:00

manage_tools.py

Add all the necessary dependency requires. Note to self: fix the egg dependency resolution bug so we don't have to dot his.

2015-02-14 10:35:42 -05:00

nosetests.py

Separate framework and tool environments.

2008-04-11 20:11:21 +00:00

paster.py

There's no reliable way to use the Galaxy config file to control egg use/fetching since so many things use galaxy.eggs from outside of Galaxy, so drop the support for the config file options and rely on the environment variables only. Reverse the defaults so that eggs and fetching are enabled by default. I'll make sure that they properly get passed to the tool execution environments in the next commit.

2015-02-12 15:10:19 -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

run_selenium_tests.sh

Adding workflow tests using Selenium. These actually drive the web browser to test the Javascript UI effectively. Currently can't run under buildbot.

2009-03-27 18:55:00 -04:00

scramble.py

Fix path insertion vs appending of <galaxy>/lib for all scripts.

2015-02-12 10:34:51 -05:00

set_dataset_sizes.py

Fix path insertion vs appending of <galaxy>/lib for all scripts.

2015-02-12 10:34:51 -05:00

set_metadata.py

Cleanup related to PR#7 and affected files.

2015-03-05 09:47:14 -05:00

set_user_disk_usage.py

Refactoring of set_user_disk_usage and admin controller disk usage to use the same pgcalc

2015-02-25 12:52:47 -05:00

summarize_timings.py

Workflow scaling test infrastructure.

2015-03-25 14:54:48 -04:00

sync_reports_config.py

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

test_dist_egg.py

Add numpy egg, update bx_python egg (now with 100% more numpy) and include code that allows scrambling to depend on other eggs existing and being importable.

2010-03-15 14:35:35 -04:00

transfer.py

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

update_shed_config_path.py

Add script to update the paths to tool config files in installed repositories' metadata.

2015-01-30 12:17:01 -05:00