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?


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

Curtin University
Tel    | +61 8 9266 7516
Mob  | +61 408 004 369
Fax    | +61 8 9266 2342
Email  | e.mor...@curtin.edu.au<mailto:e.mor...@curtin.edu.au>
Web    | biomed.curtin.edu.au


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