[maker-devel] maker-devel Digest, Vol 64, Issue 4

[Ross, Eric]

It wouldn't be too difficult to run MAKER to run using something like
starcluster.

Starcluster manages the cluster and nodes for you.
http://star.mit.edu/cluster/

It's not too difficult to use.

Eric


--
Eric Ross
Bioinformatic Specialist I
Alejandro Sánchez Alvarado Laboratory
Stowers Institute for Medical Research
Howard Hughes Medical Institute
ejr at stowers.org





On 9/6/13 1:00 PM, "maker-devel-request at yandell-lab.org"
<maker-devel-request at yandell-lab.org> wrote:

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>Today's Topics:
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>   1. Re: Maker in the cloud (Barry Moore)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Thu, 5 Sep 2013 12:06:05 -0600
>From: Barry Moore <barry.moore at genetics.utah.edu>
>To: Jasmin Zohren <j.zohren at qmul.ac.uk>
>Cc: maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] Maker in the cloud
>Message-ID: <DD487D77-AA50-4124-9ADC-F1D496233903 at genetics.utah.edu>
>Content-Type: text/plain; charset="windows-1252"
>
>Hi Jasmin,
>
>Like Carson, my only significant experience with MAKER in the cloud is
>using it for our training, however, I'll add make some comments based on
>experience on the cloud with some of our other tools:
>
>There are several cloud architectures available now, but I only have
>experience with Amazon EC2, so all comments are only relevant there.
>
>I wouldn't use any of the existing MAKER AMIs.  All of them were created
>for tutorial purposes, and while they should work fine for a real
>annotation job, they will be out of date.  At the very least if you use
>one, start with it, but install current MAKER code and save it as a new
>AMI.  You can use MPI on the Amazon nodes, but it's not set up by default
>to run MPI between nodes.  That, can presumably be done but we haven't
>done it, so there may be headaches involved we just don't know for sure.
>However, you could split your input fasta into several chunks of roughly
>equal size and fire up a different EC2 node for each fasta file, then
>allow maker to use MPI to optimize parallelization on each node
>individually.  MAKER is really good at restarting if things fail, so with
>that in mind I'd suggest staring spot nodes which can be 10X cheaper than
>regularly priced nodes.  Amazon will kill a spot node as soon as someone
>comes along who is willing to pay full price, so you'd want a way (either
>manually checking and restarting nodes or scripting a AWS API solution)
>to check whether nodes finished and restart them if they did not, but you
>could save a lot of money by doing this.
>
>B
>
>On Sep 5, 2013, at 9:58 AM, Jasmin Zohren wrote:
>
>> Dear Maker developers,
>>  
>> I?ve already contacted you a while ago about my annotation of the birch
>>genome (Betula nana). As I am constantly running into problems using our
>>cluster facilities at QMUL I thought of moving into the cloud. As I am
>>rather inexperienced in cloud computing I have several questions:
>>  
>> 1.       To me it seems that there are two different Maker images on
>>EC2 ? ami-ea661f83 and ami-b10abed8 ? which one is ?the right one??
>> 2.       Can I use this Maker AMI for the annotation of a whole genome
>>or is it only suitable for the tutorial tasks?
>> 3.       Also, when I followed the steps outlined in the tutorial,
>>there seemed to be a problem with RepeatMasker. Although Maker would run
>>and produce output files, the log file stated that the contig had failed
>>after the second attempt. I launched the image on a T1.micro instance,
>>maybe that wasn?t enough computing power? Or do you have another
>>explanation for this?
>> 4.       Would it be possible to run the annotation in parallel (e.g.
>>using MPICH2) in the cloud? I?ve also recently heard about a
>>parallelisation module for use in the cloud developed by Era7, called
>>?nispero?. But I am not sure whether it is publicly available yet.
>> 5.       Do you have any experience of how long an annotation task in
>>the cloud would take and also what the expected costs would be? The
>>birch genome is only 500 MB in size and currently I am simply annotating
>>it with a SNAP trained HMM. However, in the future I will feed it with
>>RNAseq data as well.
>>  
>> Many thanks in advance and kind regards,
>> Jasmin
>>                 
>>                 
>> -----------------------------
>> Jasmin Zohren
>> PhD student in the INTERCROSSING ITN
>> Queen Mary University of London
>>  
>> intercrossing.wikispaces.com
>> evolve.sbcs.qmul.ac.uk
>>  
>> _______________________________________________
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>
>Barry Moore
>Research Scientist
>Dept. of Human Genetics
>University of Utah
>Salt Lake City, UT 84112
>--------------------------------------------
>(801) 585-3543
>
>
>
>
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