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-...@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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/