> On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks
> wrote:
>
>> Scalability issues are more likely to arise on the back end than the front
>> end, so you'll want to ensure that you have enough compute nodes. BWA uses
>> four nodes by default--Enis, does the cloud config change this
>> parame
On Fri, Nov 18, 2011 at 12:56 AM, Jeremy Goecks wrote:
> Scalability issues are more likely to arise on the back end than the front
> end, so you'll want to ensure that you have enough compute nodes. BWA uses
> four nodes by default--Enis, does the cloud config change this parameter?--so
> you
Clare
I wonder if you would be open to share the details of your setup and what you
had to do for this once you are done. I think it would be incredibly useful to
community (at least it would be for me ;-))
Thanks!
On Nov 17, 2011, at 5:14 PM, Clare Sloggett wrote:
> Hi Enis, Jeremy,
>
> Than
Hi Enis, Jeremy,
Thanks, that's really helpful! Jeremy do you remember what kind of
instance you used per node, e.g. Amazon's 'large' (2 core / 4ECU /
7.5GB) or 'xlarge' (4 core / 8ECU / 15GB)? This would be a good sanity
check for me.
Enis when you say a lot of memory, would you consider the 15G
Hi Franzi,
You have one too many hg19 in there. The fields go like:
so:
hg19hg19hg19 /drive1/galaxy/reference/hg19/sam_index/hg19_ref.fa
gatk
But do note that these tool integrations are still undergoing active
development. Please report bugs if you encounter a
A peculiar bug, presented for your input:
A colleague has built a few tools and is trying to incorporate them into
a workflow. However:
1. When he creates an new empty workflow, edits it and adds the
tools, they appear without inputs (i.e. the icons/boxes on the diagram
have no input "so
Hi Metge,
Thank you for your kind comments!
The GATK tool wrappers are still in an early beta stage of development.
Because of this, we are not ready to support set-up in local instances yet.
If you have functionality input for the version on our Test server,
general feedback is welcomed on
> Jeremy (from the team) ran a similar workshop several months ago and used
> some resource intensive tools (e.g., Tophat). We were concerned about the
> same scalability issues so we just started 4 separate clusters and divided
> the users across those. The approach worked well and it turned o
> Thanks for your help. I'm mapping reads from one organism to a related but
> different organism, so some of the parameters I'd like to adjust are to relax
> mapping stringency -specifically:
>
> -n 3 (allow 3 mismatches in seed)
> -e 250 (allow cummulative phred score of 250 [or some other val
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