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 <E.Morgan(a)curtin.edu.au>
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?
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