Hi Raj,

The GATK tool wrappers are still in Beta and are currently under redesign.

Since this question is about a local install, it is probably better for the galaxy-dev@bx.psu.edu mailing list. When you write in (new thread, please), could you please clarify a bit more? Do you need help with installing native indexes for GATK? Or do you want to re-use indexes generated after a custom genome/other inputs are used (not a current feature, but maybe you want feedback from other developers)?

Thanks!

Jen
Galaxy team

On 7/3/12 11:53 PM, Praveen Raj Somarajan wrote:

All,

 

It is noticed that Galaxy/GATK indexes reference fasta & dbSNP file everytime when it runs. Re-indexing takes time (~10min), hence it affects overall run time when it use for multiple times. However, this could be avoided by reusing the available index. Here is the snapshot of the log:

 

INFO  11:43:57,365 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-21-g30b937d, Compiled 2012/02/01 19:01:14

INFO  11:43:57,365 HelpFormatter - Copyright (c) 2010 The Broad Institute

INFO  11:43:57,365 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki

INFO  11:43:57,366 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa

INFO  11:43:57,367 HelpFormatter - ---------------------------------------------------------------------------------

INFO  11:43:57,429 GenomeAnalysisEngine - Strictness is STRICT

INFO  11:43:57,432 ReferenceDataSource - Index file /tmp/tmp-gatk-6jlUfH/gatk_input.fasta.fai does not exist. Trying to create it now.

PROGRESS UPDATE: file is 15 percent complete

PROGRESS UPDATE: file is 28 percent complete

PROGRESS UPDATE: file is 91 percent complete

INFO  11:45:32,231 ReferenceDataSource - Dict file /tmp/tmp-gatk-6jlUfH/gatk_input.dict does not exist. Trying to create it now.

INFO  11:45:54,262 SAMDataSource$SAMReaders - Initializing SAMRecords in serial

INFO  11:45:54,280 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02

INFO  11:45:54,304 RMDTrackBuilder - Creating Tribble index in memory for file /tmp/tmp-gatk-6jlUfH/input_dbsnp_0.vcf

INFO  11:48:05,910 RMDTrackBuilder - Writing Tribble index to disk for file /tmp/tmp-gatk-6jlUfH/input_dbsnp_0.vcf.idx

 

Do we have any option/alternate in Galaxy to avoid this re-indexing at /tmp, as I have already built the index for reference and dbSNP.

 

Look forward to any suggestions.

 

Thanks,

Raj

 


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