galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00

T

John Chilton 1d672447df Update lwr_client through https://bitbucket.org/jmchilton/lwr/commits/3034b5cb789a6c96b005b838542c6e7c34c2faea .

UChicago reported some issues with the use of mmap in the LWR client for large files. To get around this, I have implemented an optional alternative transport layer for the LWR client that is backed by pycurl instead of urllib2. This can be enabled by setting the environment variable LWR_CURL_TRANSPORT=1 for the Galaxy process. If LWR_CURL_TRANSPORT is set, the python pycurl package must be installed.

2013-02-07 14:18:33 -06:00

contrib

Fix check_galaxy for recent framework changes.

2012-11-27 15:57:05 -05:00

cron

Added script to update NCBI builds list, replaced Broad data source with direct URL, cleaned up help text.

2012-08-23 16:36:58 -04:00

database

Add tool search to workflow editor. Also standardize tool panel structure and style so that it is the same in both the main interface and in the workflow editor; workflow editor now uses styles in tool_menu.css as well.

2010-09-20 13:28:16 -04:00

display_applications

genetrack: Purge all genetrack support (since it no longer exists), other than leaving filetype for backward compatibility

2013-02-03 23:21:17 -05:00

doc

Sphinx Doc: Remove enable_api step from the api quickstart as it is no longer necessary.

2013-01-18 10:26:57 -05:00

external_service_types

Fixes for transferring files from external services using the http protocol. Automatic file transfers from Pac Bio SMRT Portal are functional for version 1.1.0.

2011-04-14 16:42:12 -04:00

lib

Update lwr_client through https://bitbucket.org/jmchilton/lwr/commits/3034b5cb789a6c96b005b838542c6e7c34c2faea .

2013-02-07 14:18:33 -06:00

locale

Modify some string in Mako templetes for complete i18n support.

2011-11-24 23:56:36 +08:00

openid

Allow GenomeSpace OpenID provider for log in.

2012-04-13 15:07:07 -04:00

scripts

core: add PasteDeploy dependency back, used inside Paste#httpserver

2013-02-01 17:30:58 -05:00

static

history panel: fix to hda update logging typo

2013-02-06 12:05:56 -05:00

templates

2013-02-07 13:26:42 -05:00

test

Bugfixes for tool shed functional test scripts.

2013-02-05 16:05:33 -05:00

test-data

Add parameter to filtering tool to optionally skip header lines. Add test for new parameter usage as well.

2013-01-29 10:37:16 -05:00

tool-data

genetrack: Purge all genetrack support (since it no longer exists), other than leaving filetype for backward compatibility

2013-02-03 23:21:17 -05:00

tools

Subtract query tool: make ignoring empty end columns and whitespace optional.

2013-02-07 14:46:49 -05:00

.hgignore

Merged in jmchilton/galaxy-central-hgignore-fixes (pull request #100 : Add more commonly generated Galaxy runtime files to .hgignore.)

2013-01-15 17:09:33 -05:00

.hgtags

Added tag release_2013.01.13 for changeset a4113cc1cb5e

2013-02-02 14:10:47 -05:00

buildbot_setup.sh

Add shed_tool_data_table_conf.xml.sample to buildbot_setup.sh.

2012-11-07 21:16:17 -05:00

community_wsgi.ini.sample

Uncomment the default sqlite database connection string in community_wsgi.ini.sample.

2013-01-31 11:39:12 -05:00

create_db.sh

Allow command-line creation of initial database

2011-11-18 12:41:27 -08:00

datatypes_conf.xml.sample

Backout 3189a1bf18af

2013-02-04 06:43:35 -05:00

demo_sequencer_wsgi.ini.sample

Add the config for the demo sequencer.

2010-12-10 13:30:24 -05:00

dist-eggs.ini

Provide mercurial as an egg for tool shed operations.

2012-04-23 13:20:29 -04:00

distributed_object_store_conf.xml.sample

Object Store: Store the backend object store's ID in the database when using the distributed object store.

2012-01-09 10:06:23 -05:00

eggs.ini

eggs: Update Paste and PasteDeploy

2013-02-04 23:30:32 -05:00

external_service_types_conf.xml.sample

Renamed sequencer to external_service and sequencer_type to external_service_type.

2011-01-07 16:12:36 -05:00

extract_dataset_parts.sh

The "How to Cite Galaxy" link was being read from screencasts_url, not citation_url.

2011-11-02 16:39:08 -04:00

LICENSE.txt

Reindented license text to make it render better at bitbucket.

2013-01-11 16:00:01 -08:00

manage_db.sh

Fix for sqlalchemy-migrate scripts so they will function across webapps - galaxy is the default, so no command line changes necessary when migrating the db.

2010-07-20 09:27:14 -04:00

manage_tools.sh

File missed in the change set for the re-engineered InstallManager.

2012-02-28 14:07:20 -05:00

migrated_tools_conf.xml.sample

The InstallManager is now a stand-alone appication that attempts to load the tool panel as closely as possible to the way it was loaded before tools were migrated from the Galaxy distribution to the tool shed.

2012-02-28 11:38:08 -05:00

openid_conf.xml.sample

Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed.

2012-03-23 13:41:01 -04:00

README.txt

Update README to display a compatible python version as a result of python -V.

2012-11-19 17:05:34 -05:00

reports_wsgi.ini.sample

Add 2 new sample tracking reports and 2 new workflow reports, each of which provides the total number of items per month and the total number of items per user ( per month ). Clean up the styles in the admin menu and reports menu mako templates. Clarify in the reports config that reports do not support sqlite. Render the samples checkbox ( when editing samples ) at the top of the table cell.

2011-02-14 14:54:07 -05:00

run_community.sh

Automatically create missing required tool shed files from samples when startign the tool shed server.

2013-01-31 11:47:32 -05:00

run_demo_sequencer.sh

Add a sequencer emulator webapp for demonstration purposes.

2010-12-03 11:43:08 -05:00

run_functional_tests.sh

Tool shed functional tests for complex repository dependencies, detection and setting of metadata for invalid repository dependencies. Fixes for detecting and displaying invalid repository dependencies.

2013-02-04 11:51:42 -05:00

run_galaxy_listener.sh

sample tracking data transfer mechanism streamlined.

2010-11-07 19:46:59 -05:00

run_reports.sh

Improvements to reports management script (run_reports.sh) to enable managing the reports app from CloudMan. These enhancements are all "optional", the default behavior of run_reports.sh is unchanged.

2012-09-21 22:04:15 -05:00

run_tool_shed_functional_tests.sh

Add the framework components to enable creating a functional test framework for the tool shed.

2012-11-13 13:49:09 -05:00

run_unit_tests.sh

Fix unit tests failing on missing dependencies in job runners

2011-02-16 13:48:14 -05:00

run.sh

Maintain entries for Galaxy's ToolDataTableManager acquired from installed tool shed repositrories that contain a valid file named tool_data_table_conf.xmnl.sample in a separate config file name shed_tool_data_table_conf.xml. This will ensure that manual edits to the original tool_data_table_conf.xml will not be munged when Galaxy's tool shed installation process automatically adds entries into the file. This enhancement alos includes a bug fix where ToolDataTableEntries that should have been persisted to the XML file were not being handled correctly.

2012-11-07 16:36:28 -05:00

set_metadata.sh

Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES

2010-03-01 15:41:30 -05:00

setup_rabbitmq.sh

adding setup_rabbitmq.sh script.

2010-10-27 12:36:56 -04:00

shed_tool_conf.xml.sample

Add new sample config to point to tools installed from a tool shed and add additional directories for checking/creating at startup.

2011-09-06 13:41:06 -04:00

shed_tool_data_table_conf.xml.sample

2012-11-07 16:36:28 -05:00

tool_conf.xml.main

Add MouseMine datasource tool provided by Howie Motenko (Howie.Motenko@jax.org).

2013-02-06 17:34:36 -05:00

tool_conf.xml.sample

Add MouseMine datasource tool provided by Howie Motenko (Howie.Motenko@jax.org).

2013-02-06 17:34:36 -05:00

tool_data_table_conf.xml.oldlocstyle

Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc)

2010-11-17 11:32:45 -05:00

tool_data_table_conf.xml.sample

Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.

2012-11-26 10:18:47 -05:00

tool_list.py

minor whitespace updates, tab/space consistency

2011-07-22 15:17:26 -05:00

tool_sheds_conf.xml.sample

Enhance Galaxy tool initialization to do the following:

2011-09-02 14:57:33 -04:00

universe_wsgi.ini.sample

Make Galaxy Q&A URL optional and disable by default.

2013-01-03 09:43:53 -05:00

README.txt

GALAXY
======
http://galaxyproject.org/

The latest information about Galaxy is always available via the Galaxy
website above.

HOW TO START
============
Galaxy requires Python 2.5, 2.6 or 2.7. To check your python version, run:

% python -V
Python 2.7.3

Start Galaxy:

% sh run.sh

Once Galaxy completes startup, you should be able to view Galaxy in your
browser at:

http://localhost:8080

You may wish to make changes from the default configuration.  This can be done
in the universe_wsgi.ini file.  Tools are configured in tool_conf.xml.  Details
on adding tools can be found on the Galaxy website (linked above).

Not all dependencies are included for the tools provided in the sample
tool_conf.xml.  A full list of external dependencies is available at:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies