galaxy

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

T

Ross Lazarus 5b2e7947ea Fixed sam_merge.xml to call Picard MergeSamFiles.jar so metadata can be propagated through to the new merged bam from all the individual files - the samtools version of merge would require this to be done separately and passed in with the -h option whereas Picard does it automatically. Added one more test. Interesting that the test for that tool has been failing to correctly pass metadata but passing the buildbot anyway. Thanks to Camille Stephan for pointing out the bug.

Changes to rgManQQ so the user can obtain a decent pdf image. When millions of points are plotted, these are humongous so GS is called to compress the resulting pdf and they are now of reasonable size. PDF's are now linked from the thumbnails. Some minor fiddling with point size on the Manhatten plots so the intersting ones are a little more obvious.

Minor tweak to twilltestcase.py so composite file components are copied correctly to the directory specified by GALAXY_TEST_SAVE. This makes updating test artefacts much simpler because running tests with GALAXY_TEST_SAVE pointing somewhere will now save every tested output file.

2011-08-04 12:43:30 +10:00

contrib

Add Assaf Gordon's collect_job_timings.sh script.

2011-07-21 13:55:24 -04:00

cron

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

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

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

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

Workflows: Same fix as previous, but for rename_async...

2011-08-03 02:09:42 -04:00

locale

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

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

scripts

Bugfix for the offline egg packaging script.

2011-08-03 10:13:01 -04:00

static

Update GMAJ: fixes a ClassCastException that was encountered on Macs running Java 1.6.

2011-08-02 16:05:55 -04:00

templates

Add simple display option to data libraries that omits certain columns... unclutters LibraryDataset parameter UI

2011-08-03 13:54:28 -04:00

test

Fixed sam_merge.xml to call Picard MergeSamFiles.jar so metadata can be propagated through to the new merged bam from all the individual files - the samtools version of merge would require this to be done separately and passed in with the -h option whereas Picard does it automatically. Added one more test. Interesting that the test for that tool has been failing to correctly pass metadata but passing the buildbot anyway. Thanks to Camille Stephan for pointing out the bug.

2011-08-04 12:43:30 +10:00

test-data

Add missing test files

2011-06-10 20:10:09 -04:00

tool-data

Update annotation profiler tool sample configuration file.

2011-07-07 12:13:49 -04:00

tools

2011-08-04 12:43:30 +10:00

.hgignore

Change many tool shed methods to use the mercurial api. Fix 2 bugs introduced when email alerts were added - unauthenticated users can once again browse categories / repositories.

2011-06-28 10:24:49 -04:00

buildbot_setup.sh

Add GATK tool-data to buildbot_setup.sh links.

2011-05-12 12:20:52 -04:00

community_wsgi.ini.sample

Eliminate all suport for tool / tool suite archives from the tool shed. Yikes!

2011-06-02 15:18:35 -04:00

datatypes_conf.xml.sample

Add an altered version of Jelle Scholtalbers' enhancement code to support uploding various image data types. I've moved some of the code components around from Jelle's version, and added some fixes. The cod ein the new image_util.py file enables detections of images types without the need to create a new Image() class.

2011-07-27 16:14:15 -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

Update links to reflect Galaxy Wiki moving away from Bitbucket.

2011-07-18 18:10:55 -05:00

eggs.ini

Update links to reflect Galaxy Wiki moving away from Bitbucket.

2011-07-18 18:10:55 -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

Update links to reflect Galaxy Wiki moving away from Bitbucket.

2011-07-18 18:10:55 -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

Remove hardcoding of universe_wsgi.ini, fixes issue #358 (except for the sample cleanup scripts which, as samples, are expected to be modified by the site anyway).

2011-06-08 12:10:51 -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

tool_conf.xml.main

minor whitespace updates, tab/space consistency

2011-07-22 15:17:26 -05:00

tool_conf.xml.sample

2011-08-04 12:43:30 +10:00

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

Added color-space Tophat wrapper

2011-06-24 16:55:43 -04:00

tool_list.py

minor whitespace updates, tab/space consistency

2011-07-22 15:17:26 -05:00

universe_wsgi.ini.sample

Merge API run_as changes from John Duddy.

2011-08-03 00:34:27 -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://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies