galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-13 00:44:55 +08:00

T

Dannon Baker 5f3b33fff5 Shift management of the interaction between workflow outputs and HideDatasetActions to the front end editor.

This resolves the issue with multiple HideDatasetActions being created.
Existing workflows displaying multiple HideDatasetActions per step on the Run Workflow screen will persist.
These extra HideDatasetActions are harmless, but a simple edit workflow -> save will remove them.

2010-11-01 17:08:50 -04:00

contrib

add multiprocess.sh example script for running multiple galaxy processes. instructions coming later.

2010-05-20 17:00:12 -04:00

cron

POSIXize/Bournize updateucsc.sh.sample

2009-09-10 17:31:05 -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

Add support for displaying BAM files at Ensembl

2010-10-06 11:03:28 -04:00

lib

Shift management of the interaction between workflow outputs and HideDatasetActions to the front end editor.

2010-11-01 17:08:50 -04:00

locale

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

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

scripts

Added validation checks in the data transfer script for sample tracking

2010-10-29 15:24:30 -04:00

static

Shift management of the interaction between workflow outputs and HideDatasetActions to the front end editor.

2010-11-01 17:08:50 -04:00

templates

Shift management of the interaction between workflow outputs and HideDatasetActions to the front end editor.

2010-11-01 17:08:50 -04:00

test

sample tracking functional tests are fixed

2010-10-15 12:49:21 -04:00

test-data

Updated test outputs for pdf/image output tools that differ slightly on updated dependencies.

2010-09-29 17:25:31 -04:00

tool-data

Introduce blastdb_p.loc for protein BLAST databases

2010-09-21 17:05:24 +01:00

tools

More tweaking of lines_diff for cuffdiff test.

2010-11-01 13:46:31 -04:00

.hgignore

Fixed creation of new tracks, missing template-generated css for trackster, add .DS_Store, *.rej and *.orig to hgignore

2010-07-12 14:59:11 -04:00

buildbot_setup.sh

New hyphy nj tree test output for ps2pdf version standardized across all systems, and fix for the wig_to_bigwig test.

2010-09-29 23:55:43 -04:00

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

Add basic support for bowtie indexes as a datatype (bowtie_base_index, bowtie_color_index), available via datatype conversion. Currently, the indexes need to be converted manually from the FASTA file before use in bowtie, but they can be reused.

2010-10-07 16:59:41 -04:00

dist-eggs.ini

Minor fixes for scrambling and dist-scrambling

2010-08-17 09:29:38 -04:00

eggs.ini

Fix for a bug I introduced in NoseHTML changes.

2010-10-23 14:27:50 -04:00

LICENSE.txt

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

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

Makefile

Remove outdated about.rst/html.

2010-06-30 11:09:14 -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

MANIFEST.in

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

README.txt

Update the README.txt (just an excuse to trigger the bitbucket->buildbot connection since it should be fixed)

2010-08-18 15:13:23 -04:00

reports_wsgi.ini.sample

Enhancements for the reports webapp:

2010-05-28 16:30:16 -04:00

run_community.sh

Framework for the Galaxy Community Space.

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

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

lims:

2010-04-21 10:41:30 -04:00

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

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.sh

Remove builds.txt from source control - use builds.txt.sample instead and copy it over if you don't have one

2010-05-10 12:50:09 -04:00

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

setup.sh

Added missing Bowtie color loc file to setup.sh

2010-08-20 11:16:27 -04:00

tool_conf.xml.main

Add RNA-seq tools -- Tophat + Cufflinks suite -- to main.

2010-10-20 15:14:25 -04:00

tool_conf.xml.sample

Add RNA-seq tools -- Tophat + Cufflinks suite -- to main.

2010-10-20 15:14:25 -04:00

tool_data_table_conf.xml.sample

Add BFAST Mapper tool and wrapper.

2010-08-18 16:52:06 -04:00

tool_list.py

add test section option

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

transfer_datasets.ini.sample

Added setup script to configure RabbitMQ

2010-10-26 23:04:22 -04:00

universe_wsgi.ini.sample

Added setup script to configure RabbitMQ

2010-10-26 23:04:22 -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

Before starting Galaxy for the first time, please run the setup script:

% sh setup.sh

If setup.sh finishes successfully, you can then proceed to starting 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