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
5657e61320
Misc tool cleanup: eliminated all references to python2.3 / python2.4, imported galaxy eggs in several missed tools. Commented Pattern Matching tool section from tool_conf.xml.sample since tool is not functional. Added job runner info for short read tools in universe_wsgi.ini.sample.
2008-04-25 13:04:55 +00:00
Nate Coraor
7560751dc8
Separate framework and tool environments.
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Whether running locally or via PBS, $PATH should now be handled in your
user's environment.
This also fixes problems like PYTHONPATH on the new blast nodes being
wrong (because they are x86_64 and the frontends are i686).
Note that you can actually start Galaxy without having an eggs dir now.
2008-04-11 20:11:21 +00:00
Greg Von Kuster
af3b0669aa
Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.
2008-03-28 15:24:50 +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
34ba38d50a
More tool code cleanup, more informative messages, forgot to reset tool id in extract genomic dna tool.
2008-03-10 17:40:31 +00:00
Greg Von Kuster
302b7d880a
Extract genomic DNA will now result in warnings rather than error conditions in most cases.
2008-03-06 20:55:06 +00:00
Greg Von Kuster
ef29221209
Fix for gencode_partition tool, warnings should not result in job error.
2008-03-04 18:32:21 +00:00
Greg Von Kuster
4dd1f044e1
Removed tool version directiories for some of the tools...the rest soon.
2008-03-03 16:14:06 +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
72bfcf8281
- Fixed the MetadataMissingValidator and added a new UnspecifiedBuildValidator.
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- Added the UnspecifiedBuildValidator to several tools.
- Added is_dynamic and get_dependencies() to DataToolParameter.
2008-02-27 22:16:56 +00:00
Greg Von Kuster
cabde35b99
Added tool version directory hierarchy for encode and extract tool directories.
2008-02-22 14:18:41 +00:00
Greg Von Kuster
01378424b4
New reports app server and 1st report showing disk usage for dataset file system - still need to mess with styles a bit.
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Also fixed update_dataset_size script and delete deprecatd random_intervals code file.
2008-01-11 21:24:21 +00:00
Greg Von Kuster
31d1a87141
Better error handling in interval_to_bd_converter, a couple of other small tool fixes.
2008-01-07 18:49:12 +00:00
Greg Von Kuster
637c9f02c4
Fixes for random intervals tool.
2008-01-02 21:40:59 +00:00
Greg Von Kuster
be91b8eed0
Better error handling for gencode_partition tool, also added functional test for the tool.
2008-01-02 14:47:30 +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
71d16671bc
First pass at final phase of cleaning up approach to dynamic select lists. Added a functional test to phastOdds tool. The following tools now use this latest approach to dynamic optioons:
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axt_to_fasta, phastOdds, axt_to_lav, random_intervals, extractAxt_wrapper, axt_to_concat_fasta, aggregate_binned_scores.
2007-11-16 20:08:31 +00:00
Daniel Blankenberg
3ed0408b17
Have interval readers ignore comments as well as headers.
2007-08-13 15:20:19 +00:00
Daniel Blankenberg
868c5a26b2
Update GenomicIntervalReader using tools to use NiceReaderWrapper.
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Bad lines are silently ignored.
2007-08-03 15:18:24 +00:00
Daniel Blankenberg
e427f3445b
Minor Update to Gencode paritioning. Only affects datasets which do not overlap with provided partions (i.e. non-encode regions)
2007-07-12 20:27:52 +00:00
Daniel Blankenberg
78a71d31e3
Fix for random_intervals and other tools using bx.intervals.io.GenomicIntervalReader.
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Header lines are no longer requested.
2007-07-02 15:28:46 +00:00
Ian Schenck
77f1195f7a
Changed trans->app.
2007-05-31 20:31:28 +00:00
Daniel Blankenberg
059a63ece7
Allow gencode partitioning to work across the cluster.
2007-05-09 18:18:02 +00:00
Daniel Blankenberg
c7f6284136
Remove extraneous comment
2007-03-15 20:35:48 +00:00
Daniel Blankenberg
cc4d6934bd
Random Intervals update.
2007-03-15 20:31:09 +00:00
Nate Coraor
7ac51f24fc
All of the stuff in /cache has been moved to /depot/data2.
2007-03-13 21:27:39 +00:00
Daniel Blankenberg
ee04a832dd
Random intervals bug fixes.
2007-03-12 16:23:55 +00:00
James Taylor
f788a34fca
Moving james-wsgi branch to new trunk.
2006-11-15 16:28:21 +00:00
Daniel Blankenberg