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