Greg Von Kuster
709d2e1292
Fix for get_microbial_data tool.
2008-03-26 20:55:18 +00:00
Greg Von Kuster
749f218f08
Changed GALAXY_DATA_INDEX_DIR from an environment variable to a config entry.
2008-03-25 14:09:27 +00:00
Greg Von Kuster
cd52cabd48
Eliminated hard-codes paths to locally cached data from tools, requires developers to add softlinks to development environments.
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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
Greg Von Kuster
6d80665988
Added file_size column to dataset table, requires db schema alteration:
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alter table dataset add column file_size numeric(15,0)
Also added new script update_dataset_size.py
2008-01-08 16:19:25 +00:00
Greg Von Kuster
79745f4012
Modified all tools to use the new <options> tag for dynamic select lists. Completely eliminated the <select_options> tag approach. With the exception of find_clusters_mysql, the old dynamic_options approach is not being used by any tool, although dynamic_options is still supported in parameters.py.
2007-11-29 17:04:42 +00:00
Greg Von Kuster
300d66fb11
Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.
2007-11-21 18:48:37 +00:00
Daniel Blankenberg
4cbfce361b
Add the ability to define datatypes in the configuration file.
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Datatypes are defined like:
[galaxy:datatypes]
bed = galaxy.datatypes.interval:Bed
png = galaxy.datatypes.images:Image,image/png
where the mime-type (default of text/plain) can be declared after the class name, as is seen with png.
2007-06-01 19:25:19 +00:00
Ian Schenck
7b5aa376e9
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
Daniel Blankenberg
8554c031ed
Push Microbial datasource changes onto trunk.
2007-01-10 15:23:30 +00:00
James Taylor
f788a34fca
Moving james-wsgi branch to new trunk.
2006-11-15 16:28:21 +00:00
Greg Von Kuster