> Shall I replace:
> /orig/path/hg19        hg19    hg19                    
> /depot/data2/galaxy/bowtie2/hg19/hg19
> with
> hg19   hg19    hg19   Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index

Yes, that's correct.

Finally, please email only galaxy-dev with questions about local installations; 
galaxy-user is for questions about how to use Galaxy.


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