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(a)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) ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/