Hello Carl,
Thank you very much for your help.I have some thoughts about installing my 
local galaxy :

First,download the latest source of galaxy from 
https://bitbucket.org/galaxy/galaxy-dist/ ,then install it in my local computer.
Second,install dependencies tools mentioned in 
http://wiki.galaxyproject.org/Admin/Data%20Integration successfully.
Third ,install the needed data and configure the .loc files from the following 
help of wiki page http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup.
Finally ,our installation of local galaxy overs and it works in the mass.Is it 
right ?

And I also have some confusions:
First ,How large the total needed data is ?Is all the data in 
datacache.g2.bx.psu.edu/indexes needed ?
Second, can all of these needed data be downloaded (via rsync) by the help of 
http://wiki.galaxyproject.org/Admin/Data%20Integration?
These are the most important questions I concerned about now.I am so thankful 
for some of you advice.


Thank you very much.
  





shenwiyn

From: Carl Eberhard
Date: 2013-02-23 02:42
To: shenwiyn
CC: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ?
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
Date: 2013-02-22 01:20
To: shenwiyn
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/
___________________________________________________________
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/

Reply via email to