galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-21 13:50:20 +08:00

T

Gert Hulselmans fb01c3cc96 Avoid corruption of binary files embedded in gzip, bz2 and zip archives in the upload tool.

Add an option in the upload tool to disable the conversion of universal
line endings to Posix line endings.
This is useful for avoiding corruption of uploaded files when a binary
file is contained inside a gzip, bz2 and zip archive.

This fixes bug report: https://trello.com/card/issue-with-uploaded-2bit-gz-files/506338ce32ae458f6d15e4b3/702

2013-05-27 20:55:52 +02:00

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

New RST files describing Sphinx doc for tool shed changes.

2013-04-01 14:49:17 -07:00

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

Avoid corruption of binary files embedded in gzip, bz2 and zip archives in the upload tool.

2013-05-27 20:55:52 +02:00

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

Delete the original copy of the install_repository_tools.py Galaxy API script since it has been renamed to install_tool_shed_repositories.py

2013-05-22 14:36:08 -04:00

static

Trackster: for variant track painter, only draw loci in viewing region.

2013-05-22 15:23:15 -04:00

templates

Fix recent changes to the tool shed menu to allow a logged in user to create a new repository.

2013-05-22 15:28:40 -04:00

test

Enhance the install and test framework to support testing a single changeset revision of a repository. This defaults to testing all repositories and changeset revisions determined to be installable and testable.

2013-05-24 11:26:19 -04:00

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

Improved documentation in bowtie2 loc file.

2013-02-13 11:04:54 -05:00

tools

Avoid corruption of binary files embedded in gzip, bz2 and zip archives in the upload tool.

2013-05-27 20:55:52 +02:00

.hgignore

Visualizations framework: allow users to associate custom visualizations with models, datatypes, etc. via an xml configuration file (visualizations_conf.xml)

2013-05-17 14:45:07 -04:00

.hgtags

Added tag security_2013.04.08 for changeset 2cc8d10988e0

2013-04-08 12:28:46 -04:00

buildbot_setup.sh

Added some checks, making buildbot setup more useful for standalone buildbots.

2013-04-17 15:34:32 -04:00

create_db.sh

Allow command-line creation of initial database

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

data_manager_conf.xml.sample

First pass at a plugable Data Manager. Data Managers can be defined locally or installed from a Tool Shed. TODO: Display Data Manager information in the Tool Shed. Do not install Data Managers into Tool Panel. Add tests. Write Docs.

2013-02-14 15:13:06 -05:00

datatypes_conf.xml.sample

Add interval-to-bigwig converter, which creates a bigwig of coverage data for an interval dataset.

2013-05-14 14:56:09 -04:00

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

Postgres migrations successful, model updated

2013-04-18 15:35:00 -04:00

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

install_and_test_tool_shed_repositories.sh

Improve structure of invalid tools dict. Clarify summary and detailed log output. Add check for required environment variables.

2013-03-11 13:49:12 -04:00

job_conf.xml.sample_advanced

Merged in jmchilton/galaxy-central-multi-input-tool-fixes-2 (pull request #143 )

2013-04-05 17:05:41 -04:00

job_conf.xml.sample_basic

Define and implement job destinations, an improved method for defining resources on which Galaxy will run jobs. Functionality is similar to the current system configured via "URLs" in the Galaxy config file, but job concurrency limits on a per-destination basis works (whereas per-URL limits were broken). Sample configs for the new destination system can be found in job_conf.xml.sample_*. Also, renamed ClusterJobRunner to AsynchronousJobRunner, moved worker threads to BaseJobRunner and significantly expanded both of these classes. Updated the tasks, local, lwr, and pbs runners to use destinations, and to inherit from AsynchronousJobRunner, drmaa coming shortly. This should be entirely backwards-compatible, so if you update to this revision and change nothing, your jobs should all still run exactly as they have before. Regardless, it is not recommended that you upgrade your Galaxy instance with jobs running unless you are willing to risk losing those jobs.

2013-02-07 15:31:09 -05:00

LICENSE.txt

Reindented license text to make it render better at bitbucket.

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

manage_db.sh

Change community to tool_shed in manage_db.sh notes.

2013-03-13 11:15:07 -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_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_tool_shed.sh

Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code.

2013-03-18 10:24:03 -04:00

run_unit_tests.sh

Fix unit tests failing on missing dependencies in job runners

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

run.sh

2013-02-14 15:13:06 -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_data_manager_conf.xml.sample

2013-02-14 15:13:06 -05:00

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

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

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

Fix for tool listing with run_functional_tests.sh -list, contributed by Peter Cock.

2013-04-15 10:09:51 -04:00

tool_shed_wsgi.ini.sample

Enable dynamic configuration of message box content and visibility in the wsgi .ini file. Display the configured brand, if any, in the <title> element.

2013-05-07 11:22:38 -04:00

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

Visualizations framework: allow users to associate custom visualizations with models, datatypes, etc. via an xml configuration file (visualizations_conf.xml)

2013-05-17 14:45:07 -04:00

visualizations_conf.xml.sample

Visualizations framework: allow users to associate custom visualizations with models, datatypes, etc. via an xml configuration file (visualizations_conf.xml)

2013-05-17 14:45:07 -04:00

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