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/s... https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/... These demonstrate some different ways to find the BAI file. Peter On Fri, May 22, 2015 at 3:16 AM, Eleanor Morgan <E.Morgan@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.morgan@curtin.edu.au Web | biomed.curtin.edu.au

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