Galaxy itself will call "samtools index" on BAM files, so
they should be there on disk already, See for example:

https://github.com/peterjc/pico_galaxy/blob/master/tools/samtools_idxstats/samtools_idxstats.xml

https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/samtools/samtools_idxstats/samtools_idxstats.xml

These demonstrate some different ways to find the BAI file.

Peter


On Fri, May 22, 2015 at 3:16 AM, Eleanor Morgan <e.mor...@curtin.edu.au>
wrote:

>  Hi  all,
>
>  Excuse me for the newbie question.  I am developing a local instance of
> galaxy to use primarily for teaching purposes.
> I  would like to index bam files produced in galaxy in order to view them
> in IGV.  I can’t seem to find the samtools index tool in the toolshed.  I
> can run samtools on the command line and generate indexes, but can find no
> way to add this functionality to the tool panel so that I can do it in
> Galaxy.  I also can’t find this functionality in the tool panel  (under
> Samtools or BAM tools) on usegalaxy.org.  Am I missing something?  Do I
> need to write my own tool?
>
>  Regards,
> Eleanor
>
>   Eleanor Morgan
> Senior Scientific Officer | School of Biomedical Sciences | Faculty of
> Health Sciences
>
>
> Curtin University
> Tel    | +61 8 9266 7516
>
> Mob  | +61 408 004 369
> Fax    | +61 8 9266 2342
> Email  | e.mor...@curtin.edu.au
> Web    | biomed.curtin.edu.au
>
>
>
>  Curtin University is a trademark of Curtin University of Technology.
> CRICOS Provider Code 00301J (WA), 02637B (NSW)
>
>
>
>
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