Ross makes an important point: if this installation is for more than one
user, you should install a more complete database system. This page may
help with your decisions there:
To your first question "Is all the data in
I would say you should only need the data specific to the subject of your
analyses and the tools you plan to use.
To your second question "can all of these needed data be downloaded (via
rsync)?" - perhaps you can clarify, please? We don't have any restriction
on the amount you rsync from there and you're free to download all the
data. If a problem or topic isn't covered in that wiki page, this mailing
list is a good place to ask questions related to data set up.
On Wed, Feb 27, 2013 at 5:44 AM, Ross <ross.laza...@gmail.com> wrote:
> Hi, shenwiyn
> I'd also add:
> Fourth, replace distributed default sqlite with postgresql
> to your list if it's for any serious use. Sqlite is ok for testing.
> On Wed, Feb 27, 2013 at 9:37 PM, shenwiyn <shenw...@gmail.com> wrote:
>> **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
>> 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
>> 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.
>> *From:* Carl Eberhard <carlfeberh...@gmail.com>
>> *Date:* 2013-02-23 02:42
>> *To:* shenwiyn <shenw...@foxmail.com>
>> *CC:* email@example.com
>> *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
>> 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.
>> 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 :
>>> 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/
>>> index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/
>>> index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/
>>> index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/
>>> index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/
>>> index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/
>>> index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/
>>> 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?
>>> 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?
>>> *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 ?
>>> Yes a local galaxy requires a few steps in order to install the needed
>>> The following wiki page should help get you started:
>>> Let me know if you need more information,
>>> 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?
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