Daniel Blankenberg
11a2c767c3
Rewrite of dynamic options for select lists. There are no more 'special cases' and new filters are much easier to incorporate, as neeeded.
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MAF tool interfaces now support the use of index species and all species existing in cached alignment sets.
Until main is updated and the old maf_location files can be overwritten, these symbolic links are required:
maf_index.loc -> /depot/data2/galaxy/maf_index_new.loc
maf_pairwise.loc -> /depot/data2/galaxy/maf_pairwise_new.loc
2008-05-29 17:38:46 +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
dbc9b6a403
Cleaned up data_meta filter for dynamically generated select lists.
2008-02-29 17:44:37 +00:00
Greg Von Kuster
703c916b09
Added blurb to Get ENCODE Data tools telling user data may not be current.
2008-01-14 21:39:11 +00:00
Greg Von Kuster
ab1d867915
More dynamic options cleanup. Eliminated the "tool_type" attribute, among other cleanup chores.
2007-11-30 20:08:21 +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
Greg Von Kuster
e190e6e2b0
Enhancements to the way dynamic_options work in order to enable tools using dynemic_options to function in workdflow.
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We're still supporting the current dynamic_options functionality. This is a first pass and will be cleaned up as we continue to evolve more tools to use this new approach.
Within tool configs, SelectToolParameter types now include a <select_options> tag set. Several tools have been altered to use this new approach. Other tools we enhanced to
use the ColumnListParameter type.
2007-10-19 20:42:11 +00:00
James Taylor
f788a34fca
Moving james-wsgi branch to new trunk.
2006-11-15 16:28:21 +00:00
Daniel Blankenberg