On Feb 28, 2013, at 4:05 AM, shenwiyn wrote:
> Hi everyone,
> Thank you very much for your help.
> I want to download the complete directory of galaxy data through "rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX".But It can't work.
> And then I try to via http://dan.g2.bx.psu.edu/ by http://datacache.g2.bx.psu.edu/ ,I get "502 Bad Gateway".
> So what happens? How cat I get the data? Is there another way?
> Help me please.
Hi shenwiyn,
If you are getting a specific error from rsync on the command line, could you provide that error?
Thanks,
--nate
>
> shenwiyn
>
> From: Carl Eberhard
> Date: 2013-02-27 22:28
> To: Ross
> CC: shenwiyn; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ?
> Hello,
>
> 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:
> http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=show&redirect=Admin%2FConfig%2FPerformance
>
> To your first question "Is all the data in datacache.g2.bx.psu.edu/indexes needed?", 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.
>
> Thanks,
> Carl
>
>
> On Wed, Feb 27, 2013 at 5:44 AM, Ross <ross.lazarus@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 <shenwiyn@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 computer.
> Second,install dependencies tools mentioned inhttp://wiki.galaxyproject.org/Admin/Data%20Integration successfully.
> Third ,install the needed data and configure the .loc files from the following help of wiki pagehttp://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 ofhttp://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 <shenwiyn@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 inhttp://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 <shenwiyn@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
>
>
>
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