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.
...
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.
...
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.
...
- 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
Greg Von Kuster