Hello Nik, It doesn't appear that this question has been addressed yet. On 8/19/11 3:04 PM, Nikhil Joshi wrote:

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?

The wrapped Bowtie tool in Galaxy has two modes, one uses a native index and the other creates an index from a custom reference genome provided by the user. Perhaps this is the part of the tool wrapper that you are seeing?

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!

Instructions for creating and staging NGS indexes (including Bowtie) are in this wiki, in particular see the section "Setting Up the Reference Genomes for NGS Tools": http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Hopefully you had worked this out already or this helps! Take care, Jen Galaxy team

- Nik.

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