galaxy

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

T

Wen-Yu Chung 782d7db6be Update fastq format.

Now we only support FastqSolexa variants.
If the quality scores are presented as characters,
the integer values are obtained by their ascii code subtract 64.

2008-06-06 18:52:11 +00:00

cron

Move ucsc and gbrowse data from static to tool-data/shared.

2008-06-03 18:53:26 +00:00

database

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

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

lib

Update fastq format.

2008-06-06 18:52:11 +00:00

scripts

It doesn't make sense to even distribute DRMAA_python eggs. So instead

2008-05-30 20:18:03 +00:00

static

Unseq genome for June

2008-06-04 01:13:33 +00:00

templates

More workflow and dynamic options compatibility fixes.

2008-06-05 16:35:51 +00:00

test

Requires config modification - Add Fastq sniffer, add support for fastqsolexa data type, rename convert_fatsq2fasta tool to be fastq_to_fasta_qual, add functional tests for both fastq and fastqsolexa data types, misc code cleanup.

2008-05-29 19:12:36 +00:00

test-data

2008-05-29 19:12:36 +00:00

tool-data

Move ucsc and gbrowse data from static to tool-data/shared.

2008-06-03 18:53:26 +00:00

tools

Update fastq format.

2008-06-06 18:52:11 +00:00

datatype_converters_conf.xml.sample

Update fastq format.

2008-06-06 18:52:11 +00:00

dist-eggs.ini

dist-scramble, scrambles eggs for distribution.

2008-05-02 17:05:40 +00:00

eggs.ini

Add a no_download parameter to eggs.ini so scramble-only eggs can be

2008-05-30 20:37:39 +00:00

LICENSE.txt

Moving james-wsgi branch to new trunk.

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

Makefile

Moving james-wsgi branch to new trunk.

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

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

Fix for annotation profiler, also fixed database settin gin reports confi sample.

2008-04-15 17:47:29 +00:00

Revision

Revision info

2007-02-08 20:16:16 +00:00

run_functional_tests.sh

Separate framework and tool environments.

2008-04-11 20:11:21 +00:00

run_reports.sh

Fix for current month's job report.

2008-05-23 14:13:01 +00:00

run_unit_tests.sh

Fix the unit tests.

2008-04-11 20:14:32 +00:00

run.sh

Separate framework and tool environments.

2008-04-11 20:11:21 +00:00

setup_paths.sh

Skip check_eggs.py for buildbot. If fetch_eggs.py succeeded, they're

2008-03-27 19:32:14 +00:00

setup.sh

Update pkg_resources to 0.6c8 to fix the cygwin non-executable dll

2008-04-14 19:25:35 +00:00

tool_conf.xml.main

Added Taxonomy manipulation tool section to main tool config.

2008-05-06 16:11:55 +00:00

tool_conf.xml.sample

2008-05-29 19:12:36 +00:00

tool_list.py

add test section option

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

universe_wsgi.ini.sample

Update fastq format.

2008-06-06 18:52:11 +00:00

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