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Amazon Snapshot (view source)

Revision as of 12:57, 20 May 2013

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* '''Instance size'''  (memory and number of processors). The pipeline software will require at least 4GB of memory (''type m1.medium'') and can use as many processors as is available.
 
* '''Instance size'''  (memory and number of processors). The pipeline software will require at least 4GB of memory (''type m1.medium'') and can use as many processors as is available.
   −
* '''Storage''' for the instance refers to the size for root (/) partition. This can be quite small, as little as 8GB can work. Of course if you intend to bring lots of other files/programs to the instance, you may want to increase this to something a bit larger (e.g. 30GB).
+
* '''Storage''' for the instance refers to the size for root (/) partition. This can be quite small, as little as 8GB can work. Of course if you intend to bring other files/programs to the instance, you may need to increase this to something a bit larger (e.g. 30GB).
   −
* '''Data Storage''' for the aligner or snpcaller will likely be far larger than the system you are creating.
+
* '''Data Storage''' for the aligner or SNP caller (see below)
−
You'll need to create EBS Volumes for the input and output of the aligner and snpcaller.
  −
These can be quite substantial and because of that we recommend you create separate volumes like this:
     −
* Your input FASTQ files for the aligner. This might have been done for you by some vendor when they put your FASTQ data on an S3 volume. If so, your vendor will need to provide you with the details of how to access your FASTQ files.
     −
* The output of the aligner (BAM files)
+
'''Prepare Your Instance'''
   −
* The intermediate files of the SNP caller
+
You will also want additional storage volumes for:
    +
* '''Local Storage''' for the instance refers to the size for root (/) partition. This can be quite small, as little as 8GB can work. Of course if you intend to bring other files/programs to the instance, you may need to increase this to something a bit larger (e.g. 30GB).
   −
'''Prepare Your Instance'''
+
* '''Data Storage''' for the aligner or SNP caller will likely be far larger than the system you are creating.
 +
You'll need to create EBS Volumes for the input and output of the aligner and SNP caller.
 +
These can be quite substantial and because of that we recommend you create separate volumes like this:
   −
You will also want additional storage volumes for:
+
* Your input FASTQ files for the aligner. This may have been done for you by some vendor when they put your FASTQ data on an S3 volume. If so, your vendor will need to provide you with the details of how to access your FASTQ files.
   −
* GotCloud software and reference files
+
* The output of the aligner (BAM files)
−
* Your data
  −
** Sequence data
  −
** Output of the aligner
  −
** Output of umake
     −
The '''first of these''' is a small volume based on a snapshot containing the GotCloud files you will need.
+
* The intermediate files of the SNP caller (GLF files)
−
We provide an AWS snapshot of a small volume which contains the aligner and umake software and reference files.
  −
Create an EBS volume based on our snapshot and then mount that volume on your instance.
  −
In the EC2 Management Console under ELASTIC BLOCK STORE, select Volumes -> Create Volume.
  −
In the prompt supply the size and Snapshot (based on the table below).
  −
You may take the defaults for the Volume Type and IOPS.
     −
The snapshot ID varies by zone and the release of the software. You can see the complete list of GotCloud snapshots:
+
* The final output of the SNP caller (VCF files)
    
<code>
 
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Terry Gliedt
283

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