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GotCloud is made available in various forms.
GotCloud is made available in various forms.
It is distributed as conventional packages for Ubuntu and Redhat/CentOS systems.
It is distributed as conventional packages for Ubuntu and as compress TAR files for others.
In Amazon Web Services the software is made available in a EBS (Elastic Block Store) '''Snapshot'''.
In addition the source is available from github.
In Amazon Web Services the software is made available as an Amazon Machine Instance (AMI).
If this does not work or is unacceptable for some reason, you may install the
The GotCloud software itself only requires a few packages to be installed for Ubuntu installations
(java-common default-jre make libssl0.9.8).
However, there are a number of things you may well want to do in getting your data
ready for processing (access data on S3 storage, compile GotCloud or others, or
access the EC2 application data).
Assuming this is the case, the GotCloud AMI has installed these packages on Ubunutu.
If you need to run on some other distribution, you may need to install their packages.
<code>
sudo apt-get install java-common default-jre make libssl0.9.8
sudo apt-get install libnet-amazon-ec2-perl
sudo apt-get install make g++ libcurl4-openssl-dev libssl-dev libxml2-dev libfuse-dev
</code>
You will almost certainly need to fetch and install your own reference files - regardless
of the details of the system you are using.
Finally, you'll need access to your FASTQ files - either copied to the Amazon instance
or perhaps accessible from S3 storage.
If the GotCloud instance is unacceptable for some reason, you may install the
software and reference files wherever you'd like
software and reference files wherever you'd like
(read about this in [[Pipeline_Debian_Package|Installing from a Debian package]]).
(read about this in [[Pipeline_Debian_Package|Installing from a Debian package]]).
You'll need to know some details when launching an instance:
You'll need to know some details when launching an instance:
* '''Launch an Instance''' - use any instance running 64 bit software and either an Ubuntu of any version or Redhat/CentOS 6.3 distribution.
* '''Launch an Instance''' - use the GotCloud instance running 64 bit software.
* '''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.
* '''GotCloud Volume''' (copy from GotCloud ''snapshot''). We provide an AWS snapshot of a small volume which contains the aligner and umake software and reference files. Your task is to create an EBS volume based on our snapshot and then mount that volume on your instance (see below for more precise details).
* '''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).
* '''Data Storage''' for the aligner or snpcaller 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 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)
* '''Storage''' for the instance refers to the size for root (/) partition. This can be quite small, as little as 8GB should 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).
* The intermediate files of the SNP caller
