On Fri, Nov 11, 2011 at 2:09 AM, Clare Sloggett <sloc@unimelb.edu.au> wrote:

Hi Greg & Ross,

Thanks for this!

Yes, I confused the issue by mentioning the Tool Shed, sorry - it's
the binaries themselves I need to install. Essentially I think I need
to follow the steps at
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup , but I was
wondering about mi-deployment scripts as a better way to do this, and
whether that's standard practice.

After looking through the scripts they really seem like the best
option to me - it looks like they are set up so you mostly only need
to change configuration variables to get this to work.

The scripts are mentioned on the wiki instructions but don't seem to
be the default option (they are not bundled in galaxy-dist), so I
wondered if people are usually doing it this way?

Thanks,
Clare

On Fri, Nov 11, 2011 at 2:06 AM, Ross <ross.lazarus@gmail.com> wrote:
> Clare,
>
> As Greg says, the tool wrappers exposed on Main all come with a
> mercurial checkout - but all the binary dependencies, genomic data and
> indexes do not. The tool shed is really the tool-wrapper shed - binary
> and data dependencies aren't there either.
>
> I haven't tried them but I'd guess that the deploy scripts take care
> of a lot of messy details but will probably need some work to fit your
> local setup.
>
> As to email for admin - my advice would be don't worry about it - if
> one user forgets their password you can reset it from the admin
> interface - that's the main use and if this is really a test instance,
> it's not a show stopper.

>
> On Thu, Nov 10, 2011 at 9:14 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
>> Hello Clare,
>>
>> On Nov 9, 2011, at 11:11 PM, Clare Sloggett wrote:
>>
>>> Hi all,
>>>
>>> Most of our playing around with Galaxy has been in getting it working
>>> on our local cloud, but now for the first time I'm configuring a
>>> non-cloud local install of galaxy-dist (set up as per
>>> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server)
>>>
>>> So I have some naive questions!
>>>
>>> Would it be a sensible approach to grab the tools_fabfile script from
>>> mi-deployment and use it in this case? Or should I be using the Tool
>>> Shed for installing the base set of tools?
>>
>>
>> The Galaxy distribution includes all of the tools you see on both the Penn State test and main instances. You can also get tools form the tool shed if you want - see our wiki at http://wiki.g2.bx.psu.edu/Tool%20Shed for information about how to do this. I don't think you'll need to use the tools_fabfile script from mi_deployment repo for your local instance.
>>
>>
>>>
>>> Also, if I have problems with this server sending out emails (which
>>> may be the case) am I going to run into trouble with user/password
>>> management or can I just admin everything manually? There will only be
>>> a very small number of users on this server.
>>
>> I'm not clear on this question, but you certainly shouldn't run into any problems with user / password management within Galaxy. From the Galaxy Admin interface you have the ability to "Manage users" where you can reset passwords if necessary.
>>
>>>
>>> If I have missed any good 'getting started' documentation on
>>> config/admin of a local install please point me in the right
>>> direction. I've been looking at http://wiki.g2.bx.psu.edu/Admin .
>>
>> You found the right wiki.
>>
>>>
>>> Thanks,
>>> Clare
>>>
>>> --
>>> E: sloc@unimelb.edu.au
>>> P: 03 903 53357
>>> M: 0414 854 759
>>> ___________________________________________________________
>>> Please keep all replies on the list by using "reply all"
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>>> http://lists.bx.psu.edu/
>>
>> Greg Von Kuster
>> Galaxy Development Team
>> greg@bx.psu.edu
>>
>>
>>
>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
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>>
>
>
>

> --
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;

>
>
>

--
E: sloc@unimelb.edu.au
P: 03 903 53357
M: 0414 854 759

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