Can I put in a similar question on top of this: How much resources do you need 
for re-sequencing of a mammalian genome (assembly and variant detection), one 
job at a time? E.g. how much RAM  etc. if I want the re-sequencing SAM file of 
a 30-fold coverage be done in 48 hours?
 
Gerald

Gerald Bothe
32 Plum Hill Road
East Lyme, CT 06333
(860) 451 8776


>________________________________
> From: Nikos Sidiropoulos <nikos.sid...@gmail.com>
>To: Peter Cock <p.j.a.c...@googlemail.com> 
>Cc: "<galaxy-...@bx.psu.edu>" <galaxy-...@bx.psu.edu> 
>Sent: Wednesday, September 11, 2013 8:19 AM
>Subject: Re: [galaxy-dev] Scaling and hardware requirements
>  
>
>
>Hi Peter
>
>
>It's going to be one big machine, running both Galaxy server and the jobs. 
>It's going to be a multi-process configuration. If that idea is terribly bad 
>please let me know so I can give back the feedback.  
>
>
>De novo assembly can also be for the human/mouse genome. 
>
>
>Bests,
>Nikos
>
>
>
>2013/9/11 Peter Cock <p.j.a.c...@googlemail.com>
>
>On Wed, Sep 11, 2013 at 1:03 PM, Nikos Sidiropoulos
>><nikos.sid...@gmail.com> wrote:
>>> Hi all,
>>>
>>> I have a couple of questions regarding a server setup dedicated on Galaxy.
>>>
>>> The idea is to buy a 64 core 256GB RAM server. From my experience I believe
>>> that Galaxy will be able to scale up to 64 cpu's but I would like some more
>>> feedback on this. Also, is 4GB RAM per CPU core enough for NGS data?
>>> (including de-novo assembly)
>>>
>>> Bests,
>>> Nikos
>>
>>Hi Nikos,
>>
>>Is this going to be one server both for running Galaxy (which
>>needs fairly low resources) and running jobs for Galaxy,
>>like de novo assemblies (which need high resources)?
>>
>>i.e. You have one big machine only, no cluster?
>>
>>For de novo assembly the RAM per core/CPU isn't important,
>>it is the total RAM on the machine. How much RAM you
>>need depends on which assembler you use, the organism
>>(both size and also complexity) and the volume of data.
>>
>>What you've described should be fine for bacterial assemblies
>>and smaller eukaryotes - beyond that you'll need to give
>>more details.
>>
>>Peter
>>
> 
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