Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install.
Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn <shenw...@foxmail.com> wrote: > ** > Hi Carl Eberhard, > Thank you very much for you help.I have another some questions : > First, > we need to install the needed data,for example sam_fa_indices.loc file of > SAM Tools : > index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1. > fa > index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3. > fa > index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ > ailMel1.fa > index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/ > anoCar2.fa > index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/ > apiMel2.fa > index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/ > apiMel3.fa > index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/ > aplCal1.fa > .... > so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2. > fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx. > psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? > Second, > from the needed datas mentioned in the .loc files in > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to > download too much data,can we get all these data from some website instead > of searching them on Iternet one by one? > > > Thanks, > shenwiyn > > > > ------------------------------ > > *From:* Carl Eberhard <carlfeberh...@gmail.com> > *Date:* 2013-02-22 01:20 > *To:* shenwiyn <shenw...@gmail.com> > *Subject:* Re: [galaxy-dev] all the data files in .loc files needed to > download ? > Hello, > Yes a local galaxy requires a few steps in order to install the needed > data. > > The following wiki page should help get you started: > http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup > > Let me know if you need more information, > Carl > > > > On Tue, Feb 19, 2013 at 3:59 AM, shenwiyn <shenw...@gmail.com> wrote: > >> ** >> Hi all, >> Are all the data files in .loc files needed to download and put to the right >> directory when >> we install our local galaxy? >> >> thaks >> shenwiyn >> >> ------------------------------ >> shenwiyn >> >> ___________________________________________________________ >> 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/ >> > >
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