> 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
> 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
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
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 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
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
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
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
> 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
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