opensource/galaxy: Data intensive science for everyone. - galaxy - Gitea: Git with a cup of tea

opensource/galaxy

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

T

Jeremy Goecks dc36e0beed Merge.

2011-04-05 14:16:26 -04:00

MacOS X daemon launcher:

2010-12-13 13:54:22 +10:00

Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds

2011-03-29 13:59:07 -04:00

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

Add IGV as an external display application. Contributed by Tobias Wohlfrom.

2011-03-23 09:57:06 -04:00

external_service_types

Added a new updater for number of sample datasets. The number of sample datasets now updates automatically.

2011-01-14 15:09:43 -05:00

Refactor and enhance trackster visual analytics: (a) move all visual analytics code into Tool class for encapsulation; (b) put tool outputs in appropriate history when user is rerunning his own tool; (c) enable users not logged in to run tools; (d) use tool HTML to display inputs rather than sliders.

2011-04-05 11:51:48 -04:00

Integrating i18n support provided by Mitsuteru Nakao, Takashi Hatakeyama, and Hideyuki Morita.

2009-03-17 22:46:47 -04:00

Update the check_galaxy script for the recent changes to the User controller

2011-03-24 14:33:05 -04:00

Trackster: mode is not reduced if in auto mode.

2011-04-05 14:12:39 -04:00

Another pass on Trackster filtering. Filtering now supports (a) score columns in BED and GFF and (b) GTF attributes. Refactoring so that slider behavior for dynamic tools and filters are the same.

2011-03-28 15:27:14 -04:00

Improved checking to determine if a bam file is sorted. If the version of samtools being used is 0.1.13 or newer, determination of bam sorting is now much more robust. Add a new functional test to the test_library_features script that tests uploading a library_dataset (where the file is an unsorted bam file) using a combination of 'upload_paths' and 'link_to_files'. Rename the test-data file previously named 3.bam to now be named 3unsorted.bam to clarify that it is an unsorted bam file.

2011-03-23 12:18:57 -04:00

Slight output difference on the buildbot for weblogo, hopefully the difference is static.

2011-03-23 16:42:14 -04:00

Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds

2011-03-29 13:59:07 -04:00

change to weblogo test jpg comparison and code cleanups to rgCaCo

2011-04-05 14:07:10 -04:00

.hgignore

Ignore backup files from some editors

2010-10-13 11:28:37 +01:00

buildbot_setup.sh

Generalize setup of chrom length files for buildbot.

2011-03-02 16:21:36 -05:00

community_datatypes_conf.xml.sample

Galaxy Tool Shed enhancements

2010-07-22 16:43:32 -04:00

community_wsgi.ini.sample

Community upload functionality

2010-04-23 11:30:16 -04:00

datatypes_conf.xml.sample

Remove array_tree datatype; add tabix

2011-03-31 18:58:02 -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

Remove the new/ subdirectory from the eggs repository and update the pysam egg.

2011-02-18 14:34:14 -05:00

eggs.ini

Update distutils egg to 0.7, and use the provided HTML output writer to do rst->html conversion. Remove old code that previously did this. This fixes a bug where an extra "</div>" was appended after every output, resulting in the tool config not showing in workflows, in IE.

2011-02-18 17:47:07 -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

LICENSE.txt

Spiffy new library browser interface. Also, dim datasets in your

2008-09-10 10:10:13 -04:00

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

README.txt

Remove reference to setup.sh which is no longer used.

2011-03-07 10:02:39 -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

Framework for the Galaxy Community Space.

2010-04-14 10:20:32 -04:00

run_demo_sequencer.sh

Add a sequencer emulator webapp for demonstration purposes.

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

run_functional_tests.sh

Remove old Lmap from datatypes_conf.xml.sample - now deprecated from genetics.py

2010-03-10 20:59:11 -05:00

run_galaxy_listener.sh

sample tracking data transfer mechanism streamlined.

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

run_reports.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

run_unit_tests.sh

Fix unit tests failing on missing dependencies in job runners

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

run.sh

Add external_service_types_conf.xml.sample to list of configuration files that need to be initialized by setup.sh and run.sh.

2011-01-11 09:40:42 -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

tool_conf.xml.main

reverted unintended changes to tool_conf.xml.main

2011-04-05 14:14:08 -04:00

tool_conf.xml.sample

Adding two new tool wrappers and tests - clustalw (http://www.clustal.org ) for multiple alignments and a sequence motif generator based on weblogo3 (http://weblogo.berkeley.edu ) which works on fasta files such as alignments from clustalw

2011-03-22 14:08:32 -04:00

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

Initial commit of Mosaik and Freebayes.

2011-02-23 14:01:58 -05:00

tool_list.py

add test section option

2007-10-31 19:12:00 +00:00

universe_wsgi.ini.sample

Add SGD Yeast genome Gbrowse display site.

2011-03-23 09:03:13 -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 2.4, 2.5 or 2.6. To check your python version, run:

% python -V
Python 2.4.4

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://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies