 Greg Von Kuster
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5657e61320
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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.
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2008-04-25 13:04:55 +00:00 |
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Greg Von Kuster
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af3b0669aa
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Eliminated all Python2.4 references, added necessary assert statements to ensure minimum version of Python 2.4.
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2008-03-28 15:24:50 +00:00 |
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Greg Von Kuster
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749f218f08
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Changed GALAXY_DATA_INDEX_DIR from an environment variable to a config entry.
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2008-03-25 14:09:27 +00:00 |
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Greg Von Kuster
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cd52cabd48
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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
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2008-03-21 18:31:39 +00:00 |
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Greg Von Kuster
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4dd1f044e1
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Removed tool version directiories for some of the tools...the rest soon.
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2008-03-03 16:14:06 +00:00 |
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Greg Von Kuster
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cabde35b99
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Added tool version directory hierarchy for encode and extract tool directories.
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2008-02-22 14:18:41 +00:00 |
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Greg Von Kuster
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31d1a87141
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Better error handling in interval_to_bd_converter, a couple of other small tool fixes.
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2008-01-07 18:49:12 +00:00 |
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Greg Von Kuster
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637c9f02c4
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Fixes for random intervals tool.
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2008-01-02 21:40:59 +00:00 |
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Daniel Blankenberg
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3ed0408b17
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Have interval readers ignore comments as well as headers.
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2007-08-13 15:20:19 +00:00 |
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Daniel Blankenberg
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868c5a26b2
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Update GenomicIntervalReader using tools to use NiceReaderWrapper.
Bad lines are silently ignored.
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2007-08-03 15:18:24 +00:00 |
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Daniel Blankenberg
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78a71d31e3
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Fix for random_intervals and other tools using bx.intervals.io.GenomicIntervalReader.
Header lines are no longer requested.
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2007-07-02 15:28:46 +00:00 |
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Daniel Blankenberg
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c7f6284136
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Remove extraneous comment
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2007-03-15 20:35:48 +00:00 |
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Daniel Blankenberg
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cc4d6934bd
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Random Intervals update.
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2007-03-15 20:31:09 +00:00 |
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Nate Coraor
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7ac51f24fc
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All of the stuff in /cache has been moved to /depot/data2.
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2007-03-13 21:27:39 +00:00 |
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Daniel Blankenberg
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ee04a832dd
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Random intervals bug fixes.
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2007-03-12 16:23:55 +00:00 |
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James Taylor
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f788a34fca
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Moving james-wsgi branch to new trunk.
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2006-11-15 16:28:21 +00:00 |
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