galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-16 15:45:04 +08:00

T

Greg Von Kuster 3135ffa5fc Fix for LibraryDatasetDatasetAssociation objects when created by importing a history item iinto a library, the copied_from_history_dataset_association_id will now be kept.

Add a get_display_name() method to the LibraryDatasetDatasetAssociation class.

Fix for the test_forms_and_requests.py functional test script, purge all created libraries created during the tests so following test runs will test correctly.

2010-06-02 14:24:48 -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

Removed tmp and files from svn, now automatically created via run.sh

2007-05-02 19:23:00 +00:00

display_applications

Minor cleanup for ensembl display applications and fastq masker tool.

2010-05-24 15:05:55 -04:00

lib

Fix for LibraryDatasetDatasetAssociation objects when created by importing a history item iinto a library, the copied_from_history_dataset_association_id will now be kept.

2010-06-02 14:24:48 -04:00

locale

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

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

scripts

Updates for 'Profile Annotations for a set of genomic intervals' tool. This tool will now report a 'data version'. Add a script that creates the indexes and table description xml from a UCSC database dump.

2010-04-23 11:14:26 -04:00

static

Search/select sorts only dbkey selects; others are unsorted.

2010-05-31 15:18:32 -04:00

templates

When use_remote_user = True, still display the logged in user in the User menu

2010-06-01 09:44:42 -04:00

test

Fix for LibraryDatasetDatasetAssociation objects when created by importing a history item iinto a library, the copied_from_history_dataset_association_id will now be kept.

2010-06-02 14:24:48 -04:00

test-data

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

tool-data

First pass at adding Ensembl browsers as an external display application. Two different URL generation and data attachment methods are used; one for 'old' Ensembl archives older than ~November 2008 and another for Ensembl sites using the current method. The tool-data/shared/ensembl/ensembl_sites.txt file contains the site and build information for using the current method; the tool-data/shared/ensembl/ensembl_sites_data_URL.txt file has the site and build information for when the older method is to be used.

2010-05-21 15:25:56 -04:00

tools

Update tests for pca_for_lda1 tool.

2010-05-27 11:29:20 -04:00

.hgignore

Adding rg test outputs and updated tools

2010-03-26 14:42:15 -04:00

buildbot_setup.sh

Add missing location files for buildbot

2010-05-27 12:22:27 -04:00

community_datatypes_conf.xml.sample

Community upload functionality

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

community_wsgi.ini.sample

Community upload functionality

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

datatypes_conf.xml.sample

First pass at implementing a method for allowing a maximum file size cutoff for setting optional metadata (e.g. line and sequence counts). Currently csFasta, qualsolid, and fastq make use of this option.

2010-05-24 14:15:02 -04:00

dist-eggs.ini

Update psycopg2 to 2.0.13/postgresql 8.4.2

2010-03-09 14:13:05 -05:00

eggs.ini

Branch merge

2010-05-23 08:45:01 -04:00

LICENSE.txt

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

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

Makefile

Moving james-wsgi branch to new trunk.

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

manage_db.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

MANIFEST.in

Moving james-wsgi branch to new trunk.

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

README.txt

Remove setup.py, update README.txt

2008-05-02 19:42:59 +00:00

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.sh

Add a jar directory / bin which is accessible to tool configurations by specifying e.g. '${GALAXY_DATA_INDEX_DIR}/shared/jars/FOO.jar', where FOO.jar is the desired jar which has been placed in / linked to 'GALAXY_ROOT/tool-data/shared/jars' (by default; $GALAXY_DATA_INDEX_DIR can be configured to point elsewhere [value of 'tool_data_path' configuration variable in universe_wsgi.ini]).

2010-05-27 16:01:25 -04:00

tool_conf.xml.main

add fly_modencode, worm_modencode, and wormbase tools to main

2010-06-01 11:19:30 -04:00

tool_conf.xml.sample

Add tools contributed by Chungoo Park (cxp440@psu.edu) for Principal Component Analysis, Linear Discriminant Analysis, and drawing Receiver Operating Characteristic plots.

2010-05-25 15:48:25 -04:00

tool_list.py

add test section option

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

transfer_datasets.ini.sample

LIMS data transfer:

2010-02-12 14:01:45 -05:00

universe_wsgi.ini.sample

Fixes for displaying appropriate datasets in GBrowse wormbase, modENCODE worm, and modENCODE fly.

2010-05-12 14:37:00 -04:00

README.txt

GALAXY
======
http://g2.bx.psu.edu/

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

HOW TO START
============
Galaxy requires Python 2.4 or 2.5. 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://g2.trac.bx.psu.edu/wiki/ToolDependencies