Hello Sachit,

Instructions for setting up local indexes are in our wiki here:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup

Bowtie2 is not specifically listed, but the instructions for Bowtie and Bowtie2 are nearly identical. The same indexes are used for Bowtie2 and Tophat2. When building the index, you simply replace "bowtie-build" with "bowtie2-build" in the command string and create/modify the bowtie2_index.loc file the same as you would the bowtie_index.loc file.

The Tophat2 manual has some more details about getting set up here:
http://tophat.cbcb.umd.edu/manual.html

Next time, for questions about local installs, using just the galaxy-dev@bx.psu.edu list is best (no need to post to multiple lists). If your question has been misunderstood, please send more details to clarify.

Best,

Jen
Galaxy team


On 12/12/12 3:46 AM, Sachit Adhikari wrote:
How do I add hg16 into the build-in index?  

___________________________________________________________
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:

  http://lists.bx.psu.edu/

-- 
Jennifer Jackson
http://galaxyproject.org