Greg Von Kuster cd52cabd48 Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments. ...

Galaxy developers should execute the following commands in their $UNIVERSE_HOME/tool-data directories:

ln -s /depot/data2/galaxy/alignseq.loc alignseq.loc
ln -s /depot/data2/galaxy/binned_scores.loc binned_scores.loc
ln -s /depot/data2/galaxy/blastdb.loc blastdb.loc
ln -s /depot/data2/galaxy/encode_datasets.loc encode_datasets.loc
ln -s /depot/data2/galaxy/liftOver.loc liftOver.loc
ln -s /depot/data2/galaxy/maf_index.loc maf_index.loc
ln -s /depot/data2/galaxy/maf_pairwise.loc maf_pairwise.loc
ln -s /depot/data2/galaxy/microbes/microbial_data.loc microbial_data.loc
ln -s /depot/data2/galaxy/phastOdds.loc phastOdds.loc
ln -s /depot/data2/galaxy/quality_scores.loc quality_scores.loc
ln -s /depot/data2/galaxy/regions.loc regions.loc
ln -s /depot/data2/galaxy/twobit.loc twobit.loc

2008-03-21 18:31:39 +00:00

..

bed_convert.xml

Moving james-wsgi branch to new trunk.

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

biomart_filter.py

Added file_size column to dataset table, requires db schema alteration:

2008-01-08 16:19:25 +00:00

biomart_test.xml

Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.

2007-09-27 12:24:27 +00:00

biomart.xml

Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.

2007-09-27 12:24:27 +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

More width hints for data source tools.

2007-07-05 19:20:33 +00:00

encode_import_all_latest_datasets.xml

Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.

2008-03-21 18:31:39 +00:00

encode_import_chromatin_and_chromosomes.xml

Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.

2008-03-21 18:31:39 +00:00

encode_import_code.py

Added file_size column to dataset table, requires db schema alteration:

2008-01-08 16:19:25 +00:00

encode_import_gencode.xml

Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.

2008-03-21 18:31:39 +00:00

encode_import_genes_and_transcripts.xml

Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.

2008-03-21 18:31:39 +00:00

encode_import_multi-species_sequence_analysis.xml

Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.

2008-03-21 18:31:39 +00:00

encode_import_transcription_regulation.xml

Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.

2008-03-21 18:31:39 +00:00

encode_import.py

Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.

2008-03-21 18:31:39 +00:00

encodedb_filter.py

Added file_size column to dataset table, requires db schema alteration:

2008-01-08 16:19:25 +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

Added file_size column to dataset table, requires db schema alteration:

2008-01-08 16:19:25 +00:00

hbvar.xml

Changing all tools that use 'text' as file extension to now use 'txt'. We are eliminating the use of 'text' as a file extension within Galaxy and will now use only 'txt' for Text data types.

2007-09-27 12:24:27 +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

Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.

2008-03-21 18:31:39 +00:00

microbial_import.py

Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.

2008-03-21 18:31:39 +00:00

microbial_import.xml

Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.

2008-03-21 18:31:39 +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

Added file_size column to dataset table, requires db schema alteration:

2008-01-08 16:19:25 +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_archaea.xml

More width hints for data source tools.

2007-07-05 19:20:33 +00:00

ucsc_tablebrowser_code.py

Added file_size column to dataset table, requires db schema alteration:

2008-01-08 16:19:25 +00:00

ucsc_tablebrowser_test.xml

More width hints for data source tools.

2007-07-05 19:20:33 +00:00

ucsc_tablebrowser.py

A better way to decompress UCSC gzipped files. Added functional tests for uploading binary, zipped and gzipped files. Added temp file removal to upload when exception thrown. Eliminated an unnecessary import in subtract_query.

2007-12-20 18:49:03 +00:00

ucsc_tablebrowser.xml

New layouts and style.

2007-07-05 18:39:36 +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

Enhanced upload to handle certain binary and zip files. Cleaned up the upload config. Added 4 new data types: ab1, scf, binseq.zip and txtseq.zip. Added Regional Variation section to tool_conf.xml.main.

2007-12-14 21:07:11 +00:00