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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