a61f0047f0
Better queue status messages
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4901 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 20:17:28 +00:00
7ec805bef7
should be uncommented
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4900 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-22 20:17:04 +00:00
46cd227613
Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4845 348d0f76-0448-11de-a6fe-93d51630548a
2010-12-15 14:56:12 +00:00
5dabf73039
Useful script for me
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4704 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-18 15:21:06 +00:00
7f25019f37
Inprocess functions by default now log what output files they are running for.
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On -run cleaning up .done and .fail files for jobs that will be run.
Added detection to Firehose YAML generator shell script for (g)awk versions that ignore "\n" in patterns.
Removed obsolete mergeText and splitIntervals shell scripts.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4452 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-07 19:08:02 +00:00
d841f260eb
minor improvements to queue status
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4439 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-06 14:34:35 +00:00
20b38b38f3
Updated from SnakeYAML 1.6 to 1.7.
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Added a pipeline java bean and YAML utility to serialize java beans.
Added a getFirehosePipelineYaml.sh that can pull firehose data into the pipeline yaml file format.
Updated the fullCallingPipeline.q to begin using the pipeline yaml file format for bams and reference.
More changes to come as this code gets tested out in the fullCallingPipeline.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4329 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-22 19:47:49 +00:00
1c94a73434
Fixed header generation when lines contain spaces.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4304 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-17 17:14:59 +00:00
6dcbf04378
Added gsa-firehose2
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4284 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-15 02:24:04 +00:00
8c16babe91
continuing improvements to the queueStatus helper script
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4261 348d0f76-0448-11de-a6fe-93d51630548a
2010-09-12 14:04:59 +00:00
80e31df40d
Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3965 348d0f76-0448-11de-a6fe-93d51630548a
2010-08-07 12:36:28 +00:00
be75b087ec
a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype.
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b) Add "OG" annotation to genotypes. If Beagle changes genotypes, this annotation gets the original genotype call, to ease performance comparisons. If not, this annotation gets an empty value.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3723 348d0f76-0448-11de-a6fe-93d51630548a
2010-07-06 18:33:28 +00:00
30cf78fdc0
Refactoring for a first version of scatter gather api with basic shell script implementations.
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Modified build script so that queue is cleaned during "ant clean".
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3611 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-22 18:39:20 +00:00
a08c68362e
Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1530 348d0f76-0448-11de-a6fe-93d51630548a
2009-09-04 12:39:06 +00:00
5289230eb8
Version 0.2.1 (released) of the TableRecalibrator
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-25 22:50:55 +00:00
056fcdc31c
Adding a script for diff'ing the output of samtools and the GATK for the whole genome and each individual chromosome.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@882 348d0f76-0448-11de-a6fe-93d51630548a
2009-06-02 21:19:39 +00:00
2ee2623926
Move non-java code out of playground.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@154 348d0f76-0448-11de-a6fe-93d51630548a
2009-03-23 19:31:38 +00:00
depristo
kshakir
delangel
aaron
hanna