galaxy

bed_convert.xml

Moving james-wsgi branch to new trunk.

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

biomart_filter.py

Changed trans->app.

2007-05-31 20:31:28 +00:00

biomart_test.xml

Changed behavior of history import and added BioMart test instance.

2007-05-11 13:06:30 +00:00

biomart.xml

Changed behavior of history import and added BioMart test instance.

2007-05-11 13:06:30 +00:00

echo.py

Moving james-wsgi branch to new trunk.

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

echo.xml

Moving james-wsgi branch to new trunk.

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

encode_db.xml

Parameter sanitizer can now be turned off by individual tools. Refresh behavior after tool execution can now be defined in

2007-02-21 18:01:07 +00:00

encode_import_all_latest_datasets.xml

Moving james-wsgi branch to new trunk.

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

encode_import_chromatin_and_chromosomes.xml

Moving james-wsgi branch to new trunk.

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

encode_import_code.py

All of the stuff in /cache has been moved to /depot/data2.

2007-03-13 21:27:39 +00:00

encode_import_gencode.xml

Moving james-wsgi branch to new trunk.

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

encode_import_genes_and_transcripts.xml

Moving james-wsgi branch to new trunk.

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

encode_import_multi-species_sequence_analysis.xml

Moving james-wsgi branch to new trunk.

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

encode_import_transcription_regulation.xml

Moving james-wsgi branch to new trunk.

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

encode_import.py

All of the stuff in /cache has been moved to /depot/data2.

2007-03-13 21:27:39 +00:00

encodedb_filter.py

Changed trans->app.

2007-05-31 20:31:28 +00:00

fetch.py

Moving james-wsgi branch to new trunk.

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

genbank.py

Moving james-wsgi branch to new trunk.

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

genbank.xml

Moving james-wsgi branch to new trunk.

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

hbvar_filter.py

Changed trans->app.

2007-05-31 20:31:28 +00:00

hbvar.xml

Integrated Belinda's hbvar data source. The functional test fails, but Jianbin will look at it.

2007-03-16 15:22:28 +00:00

import.py

Moving james-wsgi branch to new trunk.

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

import.xml

Moving james-wsgi branch to new trunk.

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

microbial_import_code.py

Fix for microbial data. get_html_param_map wasn't able to pass the context of the inputs into the page, which was crashing things.

2007-05-24 18:36:28 +00:00

microbial_import.py

Moving james-wsgi branch to new trunk.

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

microbial_import.xml

Fix for microbial data. get_html_param_map wasn't able to pass the context of the inputs into the page, which was crashing things.

2007-05-24 18:36:28 +00:00

show_in_ucsc_code.py

Adding tool "Display customtracks at UCSC" under Graph/Display data tab. I've added new param attributes called repeat (to repeat the param a certain number of times) and condition (to display or not display the param) and have added dynamic_options for type "data" in order to facilitate multiple data selection. These changes required certain modifications in the framework (/lib/galaxy/tools/__init__.py and parameters.py , /lib/galaxy/datatypes/interval.py and in templates/tool_form.tmpl). I ran functional tests and found no errors in any of the tools due to these modifications. There were the usual assertion errors and database errors.

2007-04-12 16:52:39 +00:00

show_in_ucsc.py

Made necessary modifications to /lib/galaxy/tools/__init__.py and added the test input and output files for "Display customtrack at UCSC" tool.

2007-04-13 15:58:39 +00:00

show_in_ucsc.xml

Adding tool "Display customtracks at UCSC" under Graph/Display data tab. I've added new param attributes called repeat (to repeat the param a certain number of times) and condition (to display or not display the param) and have added dynamic_options for type "data" in order to facilitate multiple data selection. These changes required certain modifications in the framework (/lib/galaxy/tools/__init__.py and parameters.py , /lib/galaxy/datatypes/interval.py and in templates/tool_form.tmpl). I ran functional tests and found no errors in any of the tools due to these modifications. There were the usual assertion errors and database errors.

2007-04-12 16:52:39 +00:00

ucsc_archaea.xml

There has to be at least one tool named 'ucsc_proxy' for the proxies to work. They all use the same code with different urls, but they have to submit back to the tool_runner at the end. This closes ticket 121.

2007-05-30 15:47:59 +00:00

ucsc_filter.py

Changed trans->app.

2007-05-31 20:31:28 +00:00

ucsc_proxy.py

Moving james-wsgi branch to new trunk.

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

ucsc_proxy.xml

Update UCSC direct connection to use main ucsc site. Add direct test

2007-03-21 19:52:01 +00:00

ucsc_tablebrowser_code.py

Changed trans->app.

2007-05-31 20:31:28 +00:00

ucsc_tablebrowser_test.xml

Fix ucsc test browser.

2007-03-21 19:59:58 +00:00

ucsc_tablebrowser.py

More friendly error message for when ucsc table browser is down.

2007-05-23 14:45:38 +00:00

ucsc_tablebrowser.xml

Update UCSC direct connection to use main ucsc site. Add direct test

2007-03-21 19:52:01 +00:00

ucsc_testproxy.xml

Update UCSC direct connection to use main ucsc site. Add direct test

2007-03-21 19:52:01 +00:00

upload.xml

Requires db schema change. Enhance upload tool to default to the last build used in the "current" history.

2007-04-19 20:53:16 +00:00