[maker-devel] Maker in the cloud

[Jasmin Zohren]

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 <http://intercrossing.wikispaces.com/> 

evolve.sbcs.qmul.ac.uk <http://evolve.sbcs.qmul.ac.uk/buggs/jasmin-zohren/> 

 

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