Helena Rasche
646b133bb3
Add EDAM topics to unannotated tools
2020-10-30 17:59:45 +01:00
Nicola Soranzo
ef4f5ccda4
Remove deprecated `interpreter attribute from tools <command>`
2020-03-05 12:53:09 +01:00
Martin Cech
7157600f85
fix few stray wiki links
2017-11-15 16:39:26 -05:00
Nicola Soranzo
22d4a1d8c3
dos2unix of tools/ directory. Some whitespace and PEP-8 fixes.
2015-05-15 12:40:52 +01:00
peterjc
fce2184e5b
Make tool version explicit (Job runner would assume 1.0.0)
2015-03-09 15:21:48 +00:00
Nicola Soranzo
f73d5fba6c
Fix old wiki links.
2014-04-10 20:00:45 +02:00
Nick Semenkovich
403f2c73a3
Update links to reflect Galaxy Wiki moving away from Bitbucket.
2011-07-18 18:10:55 -05:00
Kanwei Li
0f1d788690
Wiki links now point to bitbucket instead of trac
2010-01-19 18:15:27 -05:00
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.
...
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.
...
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
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
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
Helena Rasche