Can Crossbow work with local fasta data?

[Ashwinub]

Hello,

I have managed to set up a single node hadoop cluster. i installed Crossbow, Bowtie and SOAPsnp with the help of Crossbow manual. Now when i wanted to run Crossbow I realized it is fetching the data from Amazon S3 storage. Can it run on local storage. I have reference fasta file and sample fq files stored locally. Can i make reference jars of these?

Any help is much appreciated.

PS: I wanted to try out CloudBurst on hadoop. But that works only for single paired end reads. I am hoping Crossbow works on paired end data. I would love some suggestions regarding applications for mapping which can run on hadoop.

Thanks, Ashwin