Hi Enis Afgan, Thank you very much for you answer. I have some questions abount the tool of Megablast in NGS:Mapping when I download the needed indexes . There are four indexes files we need for Megablast:htgs 28-Jan-2013 ,nt 28-Jan-2013,wgs 28-Jan-2013,phiX174;but there are too many types of the indexes file in ftp://ftp.ncbi.nlm.nih.gov/blast/db/ ,for example : nt.00.tar.gz,nt.01.tar.gz,nt.02.tar.gz....I don't know the differents among these files ,and I don't which one I should choose to download.In addition ,I can't find the index file for phiX174. Could you help me and give me some advice please? Thanks. shenwiyn From: Enis Afgan Date: 2013-03-05 10:38 To: shenwiyn CC: Rafael Hernández; galaxy-dev@bx.psu.edu Subject: Re: Tools and Data Correct; certain NSG tools require additional configuration for their indices (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) On Tue, Mar 5, 2013 at 1:07 PM, shenwiyn <shenwiyn@gmail.com> wrote: Hi, I've installed Galaxy in local as what Rafael does.I want to make sure that the basic functions work successfully just depending on the necessary tools in Tool dependencies manual,and the NGS tools not only depend on the necessary tools but also some another needed data(such as indexes,and so on). thakks shenwy