Hi all,

So I am trying to add a tool to our local Galaxy, for which it needs a
bowtie-build indexed reference, but NOT the alignment.  The alignment step
is done by the tool itself (using bowtie).  My question is two-fold: One,
why does the bowtie tool do both indexing and mapping?  It seems that you
would want to have the indexing separate from the alignment so that you can
index once and then align as many times as you need.  Right now it seems
like (correct me if I am wrong) that EVERY time you do an alignment, Galaxy
will index the reference.  This seems like it is adding a lot more time to
the alignment step than is necessary.  Is this correct, or am I missing
something?  Two, so if I were to make bowtie-build into its own tool, how
could I access the files that it creates, i.e. since bowtie-build takes a
reference and a prefix as input and then creates multiple files that use the
prefix.... I guess I need to access the prefix name somehow.... any help
would be highly appreciated.  Thanks!

- Nik.
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