[Bio-Linux] GALAXY import file size limit?

[Ian Donaldson]

Thanks for your input!

Ian

________________________________________
From: Sander Granneman [sgrannem at staffmail.ed.ac.uk]
Sent: 19 January 2015 09:22
To: Bio-Linux help and discussion
Subject: Re: [Bio-Linux] GALAXY import file size limit?

Hi Ian,

I guess it all depends on what organism/kind of data they are analyzing and what kind of machine you have. A VM works just fine but RAM (and perhaps no of cpus) will likely be a limiting factor. Our analyses are mostly done on only a few million reads (CLIP) and sometimes we don’t need more than 4GB of RAM. But I would guess you would need at least 16GB of RAM if you want to do any serious analyses on mouse/human data.

For a Galaxy tutorial I guess a VM should be fine. Also if they want to use the VM to do analyses on their own machine, they could always bump up the RAM for the VM?

Sander

> On Jan 19, 2015, at 8:56 AM, Ian Donaldson <Ian.Donaldson at manchester.ac.uk> wrote:
>
> Thank you for your reply.  The aim was that people could also run their own analysis using the same VM.  Is it fair to say that the VM option is not suitable for "real world" analysis, in favour of a full install?
>
> Ian
>
> ________________________________________
> From: Sander Granneman [sgrannem at staffmail.ed.ac.uk]
> Sent: 16 January 2015 16:29
> To: Bio-Linux help and discussion
> Subject: Re: [Bio-Linux] GALAXY import file size limit?
>
> Simplest solution I guess is to use smaller bed files.
> 1.5 GB I guess equates to 10 million reads?
> Would 1 million suffice for your tutorial?
>
> Hope this helps,
>
> Sander
>
>> On Jan 16, 2015, at 4:11 PM, Ian Donaldson <Ian.Donaldson at manchester.ac.uk> wrote:
>>
>> Hi,
>>
>> I am trying out Bio-Linux 8 using the VM download.  I am having trouble importing two 1.5 GB BED files into GALAXY as the memory assigned to the VM (4GB) is max'ing out.  Can anyone recommend a usable amount of RAM to allow this sort of operation to complete?
>>
>> My aim is to give instructions to people on how to download the VM and run a GALAXY tutorial.
>>
>> Thank you,
>>
>> Ian
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>
> ------------------------------------------------------------------
> --------
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> !!! Book the dates !!!
>
> The 10th International EMBO Conference on Ribosome Synthesis will be held in Brussels, Belgium, 19-23 August 2015.
>
> Organizing committee : Sander Granneman (University of Edinburgh), Katrin Karbstein (The Scripps Research Institute, Florida), Denis Lafontaine (University of Brussels), Tom Meier (Albert Einstein College of Medicine, New York) and Joost Zomerdijk (University of Dundee).
>
> --------
>
> Sander Granneman, PhD
> Wellcome Trust RCD Fellow
> University of Edinburgh
> Institute of Structural and Molecular Biology
> Centre for Synthetic and Systems Biology (SynthSys)
> University of Edinburgh
> Max Born Crescent
> CH Waddington Building, room 3.06
> EH9 3BF
> Edinburgh
>
> Phone:
> office: +44 (0) 131 651 9082
> lab: +44 (0) 131 651 9055
>
> sgrannem at staffmail.ed.ac.uk
>
> http://sandergranneman.bio.ed.ac.uk
> http://www.csbe.ed.ac.uk/
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------------------------------------------------------------------
--------

!!! Book the dates !!!

The 10th International EMBO Conference on Ribosome Synthesis will be held in Brussels, Belgium, 19-23 August 2015.

Organizing committee : Sander Granneman (University of Edinburgh), Katrin Karbstein (The Scripps Research Institute, Florida), Denis Lafontaine (University of Brussels), Tom Meier (Albert Einstein College of Medicine, New York) and Joost Zomerdijk (University of Dundee).

--------

Sander Granneman, PhD
Wellcome Trust RCD Fellow
University of Edinburgh
Institute of Structural and Molecular Biology
Centre for Synthetic and Systems Biology (SynthSys)
University of Edinburgh
Max Born Crescent
CH Waddington Building, room 3.06
EH9 3BF
Edinburgh

Phone:
office: +44 (0) 131 651 9082
lab: +44 (0) 131 651 9055

sgrannem at staffmail.ed.ac.uk

http://sandergranneman.bio.ed.ac.uk
http://www.csbe.ed.ac.uk/
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--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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