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25 Commits (7b92cd5008a3c58f17a7523abd07c1ed764d4e98)

Author SHA1 Message Date
depristo c50f39a147 V3 of the distributed GATK. High-efficiency implementation. Support for status tracking for debugging and display. Still not safe for production use due to NFS filelock problem. V4 will use alternative file locking mechanism 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5063 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-24 16:45:07 +00:00
kshakir 6fbd18c759 Cleaning up obsolete code. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5044 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-21 16:27:35 +00:00
kshakir 8855f080c2 For the fullCallingPipeline.q: 
- Reading the refseq table from the YAML if not specified on the command line.
 - Removed obsolete -bigMemQueue now that CombineVariants runs in 4g.
 - Added a -mountDir /broad/software option to work around adpr automount issues.
 - Merged the LSF preexec used for automount into the shell script used to execute tasks.
 - Using the LSF C Library to determine when jobs are complete instead of postexec.
 - Updated queue.sh to match the changes above.
 - Updated the FCPTest to match the changes above.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5036 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-20 22:34:43 +00:00
corin af60666f5d An example template for the shell script used to run the full calling pipeline on the broad system 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5022 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-19 20:28:59 +00:00
kshakir c901fb6d70 Now populating the refseq and dbsnp in awk instead of retrieving from firehose. 
Added refseq table to the pipeline object.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5020 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-19 18:19:10 +00:00
depristo 0e089ce0b7 watch -n 30 shell/pipelineJobs.csh for those who want to watch the gsaadm's jobs progress 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4966 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-09 13:09:30 +00:00
depristo be67161b47 Deleting old shell code 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4962 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-07 21:36:16 +00:00
depristo 2448b859e4 no longer prints unnecessary table conversion failures that muck up emails. Run script now uses du not ls to display archive size 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4918 348d0f76-0448-11de-a6fe-93d51630548a
 2011-01-02 13:27:37 +00:00
depristo a61f0047f0 Better queue status messages 
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
depristo 7ec805bef7 should be uncommented 
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
depristo 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 
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
depristo 5dabf73039 Useful script for me 
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
kshakir 7f25019f37 Inprocess functions by default now log what output files they are running for. 
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
depristo d841f260eb minor improvements to queue status 
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
kshakir 20b38b38f3 Updated from SnakeYAML 1.6 to 1.7. 
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
kshakir 1c94a73434 Fixed header generation when lines contain spaces. 
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
kshakir 6dcbf04378 Added gsa-firehose2 
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
depristo 8c16babe91 continuing improvements to the queueStatus helper script 
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
depristo 80e31df40d Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am 
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
delangel 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. 
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
kshakir 30cf78fdc0 Refactoring for a first version of scatter gather api with basic shell script implementations. 
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
depristo 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! 
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
depristo 5289230eb8 Version 0.2.1 (released) of the TableRecalibrator 
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
aaron 056fcdc31c Adding a script for diff'ing the output of samtools and the GATK for the whole genome and each individual chromosome. 
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
hanna 2ee2623926 Move non-java code out of playground. 
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