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

These demonstrate some different ways to find the BAI file.


On Fri, May 22, 2015 at 3:16 AM, Eleanor Morgan <> 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  Am I missing something?  Do I need to write my own tool?


Eleanor Morgan
Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences

Curtin University
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