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58 Commits (e253f6f05d793dcd41dde40d2ae30a92ff2dfa95)

Author SHA1 Message Date
Mauricio Carneiro e253f6f05d Fixing typo in DPP 
platform and library were exchanged when rebuilding the read group information
 2011-09-01 18:13:52 -04:00
Mauricio Carneiro dc8398e165 fixing bai output for indel cleaning. 2011-08-24 15:58:34 -04:00
Ryan Poplin 8072bd9831 Updating resource bundle generation qscript for changeover to git 2011-08-08 12:35:39 -04:00
Mauricio Carneiro 2fd101135c Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-08-08 10:49:43 -04:00
Mauricio Carneiro 4d6cb33612 removing temporary bam index 
The clean bai file was left behind after the data processing pipeline was done
 2011-08-08 10:49:28 -04:00
Ryan Poplin 738e94efcb Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-08-07 17:36:45 -04:00
Khalid Shakir eaa2f16d83 When a job finishes successfully in the ShellJobRunner, mark it as DONE instead of FAILED. 2011-08-06 10:42:04 -04:00
Ryan Poplin 21dc9a5543 Adding mills/devine indel dataset to the resource bundle 2011-08-04 12:31:28 -04:00
Mauricio Carneiro aff681e407 Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-08-04 11:05:25 -04:00
Mauricio Carneiro 23ec5b94cf fixed a missing check for null 
There was a missed check for the case when you don't provide an indels vcf for the cleaner.
 2011-08-04 09:50:02 -04:00
Mauricio Carneiro 8981367307 Updating memory usage for picard programs 2011-08-03 15:48:28 -04:00
Khalid Shakir a587f38808 Fixed example unified genotyper pipeline to wrap filter expressions with quotes and use rod binding name "variant" instead of "vcf". 2011-08-03 02:21:01 -04:00
Mauricio Carneiro 2d94037ad0 Remove temporary index files (*.bai) 
some temporary index files were not being removed.
 2011-07-30 02:05:22 -04:00
Mauricio Carneiro dcf21f379a Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable 2011-07-23 12:59:53 -04:00
Mauricio Carneiro f0a6dd27a1 Renaming the plot output directory names. 2011-07-23 12:59:37 -04:00
Mauricio Carneiro 4f78025b0b Merged bug fix from Stable into Unstable 2011-07-22 14:42:04 -04:00
Mauricio Carneiro 4080e2cd88 * Added the decoy reference to the bundle under the b37 resources. 
* Updated the -svn argument to -ver since we don't use svn anymore (also updated the wiki).
 2011-07-22 14:41:22 -04:00
Khalid Shakir 59eb1f4663 Memory limits changed from Int to Double. 
Updated LSF calls to read memory units from config along with tweaks to select hosts.
Moved some common code from GridEngine and LSF to super classes.
 2011-07-21 22:57:18 -04:00
Mauricio Carneiro 9ad5c7dfa4 Resolving simple conflicts in the data processing pipeline. 
Conflicts:
	public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
 2011-07-19 08:05:11 -04:00
Mauricio Carneiro 7688bda1a6 better progress report for the DPP 2011-07-18 23:39:47 -04:00
Mauricio Carneiro 2b465ab43b * added optional 'no validation' for the Data Processing pipeline. 
* some simplifications on the picard classes
 2011-07-18 23:30:31 -04:00
Mauricio Carneiro 4cf7a2af23 Removed broad specific default paths so people from outside the broad can use it. 2011-07-18 23:25:21 -04:00
Mark DePristo 449bf1b539 Testdata for diffObjects. 
PipelineTest updated to point to MD5DB.java
 2011-07-18 10:47:03 -04:00
Mauricio Carneiro ecc8726f63 Merged bug fix from Stable into Unstable 2011-07-17 18:10:18 -04:00
Mauricio Carneiro 1af76736b9 Guarantees that the list of files will always be in the same order. 2011-07-17 11:41:34 -04:00
Mauricio Carneiro 5cb5a4ec75 Merged bug fix from Stable into Unstable 2011-07-16 00:23:59 -04:00
Mauricio Carneiro dd92a14b40 Made extra indel VCF optional but DBSNP mandatory. 2011-07-16 00:23:35 -04:00
Mauricio Carneiro 2fa5dbb0fe Merged bug fix from Stable into Unstable 2011-07-16 00:15:19 -04:00
Mauricio Carneiro ed55182a4c Removing Broad specific paths from parameters and making them required. This should make it unambiguous for people inside and outside the Broad to use the DataProcessingPipeline (as per request in the GetSatisfaction) 2011-07-16 00:09:00 -04:00
Mauricio Carneiro 43bd45fcad Merged bug fix from Stable into Unstable 2011-07-15 19:40:02 -04:00
Mauricio Carneiro fd1df31ef0 changing the output directory names for Analyze Covariates 2011-07-15 19:39:42 -04:00
Mauricio Carneiro aa30f416a3 Resolving conflicts 
Conflicts:
	private/scala/qscript/depristo/ExomePostQCEval.scala
	private/scala/qscript/depristo/PostCallingQC.scala
	private/scala/qscript/org/broadinstitute/sting/queue/qscripts/archive/ExomePostQCEval.scala
 2011-07-15 16:21:42 -04:00
Mauricio Carneiro 224d373997 No need to double overload the file constructor 2011-07-15 15:19:10 -04:00
Mauricio Carneiro 7b7d40d5d9 A better name for the qscript utilities. Throw here every method you find yourself repeatedly implementing in your qscripts! 
Refactoring appropriately.
 2011-07-15 14:34:50 -04:00
Mauricio Carneiro a670d6420a Refactoring Qscript utils into queue general utils package. 2011-07-15 14:31:43 -04:00
Mauricio Carneiro f19862a643 Fixing conflicts. 2011-07-14 17:13:31 -04:00
Mauricio Carneiro 43c6a8565b looks better now. 2011-07-14 17:10:44 -04:00
Mauricio Carneiro 09ffe277ae Added a qscripts util package with some utility functions commonly shared across queue scripts. Refactored some of my public scripts to use it in an effort to make queue scripts more reusable and "supportable". 2011-07-14 17:09:35 -04:00
Mauricio Carneiro 4f8230c750 Merged bug fix from Stable into Unstable 2011-07-14 16:44:57 -04:00
Mauricio Carneiro 9f5180ab05 Recalibrates a list of bam files allowing multiple bams to be recalibrated out of a single 'mother' queue job. 2011-07-14 16:42:17 -04:00
Mauricio Carneiro df996a1a73 more progress report for the Data Processing Pipeline. 
Bam lists can now have empty lines, comments and whitespaces anywhere.
 2011-07-13 14:53:58 -04:00
Mauricio Carneiro e2f2917bd2 Merged bug fix from Stable into Unstable 2011-07-13 13:00:55 -04:00
Mauricio Carneiro ff4e31c554 Changing the file names as per Kris request. 2011-07-13 12:59:18 -04:00
Khalid Shakir e93052a51e When generating the QGraph, don't regenerate if there aren't scatter/gather jobs. 
Fixed a display issue with the number of milliseconds that Queue has tried to contact LSF.
 2011-07-11 19:17:58 -04:00
Mauricio Carneiro 5298e3a942 Making the outputDir optional. Default = ./ 2011-07-05 16:30:41 -04:00
Mauricio Carneiro 7d3dfdfdf2 Updating the MDCP to use the classpath for the GATK jar, removing -gatk parameter. 2011-07-05 16:30:10 -04:00
Khalid Shakir b6bc64a0c8 Cleanup of the utils.broad package. 
Using Picard IoUtils on sample names.
 2011-07-01 20:47:03 -04:00
David Roazen 546e7777fa Re-fixing paths in pipeline tests after example qscripts got moved. 2011-07-01 16:39:10 -04:00
Mauricio Carneiro b0fb63e20a moving the example scala scripts to the qscripts package. 2011-07-01 16:14:59 -04:00
Mauricio Carneiro d19351f71a Added capability of running multiple bam files in the same directory. 2011-07-01 16:02:28 -04:00