Update utilities to get GATKRunReports

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-- Critical bugfix: the GATK run reports magically changed names from something like GATK-run-report to GATKRunReport in GATK 2.4.  All GATK logs from 2.4 onwards were being eaten by the scripts that download logs, so the GATK usage is actually much much higher than our logs have suggested.  Looking forward to seeing some real numbers.  Unfortunately the error occurred so early in the downloading process that we actually deleted away these logs, so they cannot be recovered
-- Added a step in the downloader that archives the raw, unprocessed files so we can recover from such problems in the future
-- The s3 download scripts now download to /local/dev/GATKLogs so will only work on gsa4, but this is ok as this is better than taking forever to get the logs to the isilon.
-- Turn off some crazy debugging output from the downloader that was actually masking me from seeing the issue each night
-- Make analyzeRunReports.py robust to svn version abominations
-- Use python-2.6 in runGATKReport.csh

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This commit is contained in:

Mark DePristo 2013-06-13 17:08:34 -04:00

parent ac346a93ba

commit a057f37331

Show all changes Ignore whitespace when comparing lines Ignore changes in amount of whitespace Ignore changes in whitespace at EOL

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