Personal Genomics/Deploying a DAS server for Dummies/6 Easy steps

Easy Deployment of DAS server for Personal Genotype data to the Amazon Cloud

Easy steps to have your personal genomic data available as a DAS source:

1) Set up an Amazon Web Services Account (AWS) which is as easy as setting up a normal amazon shopping account on the web.

2) Download and unpack a war file from this url

3) replace the person1.txt file with your own genotype data file (make sure there are no headers – just the data)

4) edit the person1 element in MydasServerConfig.xml file so that the query uris match the url your data will be served from

5) repackage the file into a .war file rename it to mychoiceofname.war

6) Upload to Elastic Beanstalk in the amazon cloud (easy web user interface and just accept defaults).

More detailed instructions:

1) Sign up to amazon aws here http://aws.amazon.com/. You will be asked to put in your credit card details, but costs are likely to  be minimal ( a guess would be anywhere from no charge to $6 per month in extreme use cases). When I signed up amazon gave free usage for elastic beanstalk (the service we want to use) for the first year – this offer may still be available. Even if they were charging me the charges were between 0-11 cents per  month.

2) click on this link to download the MyDasTemplate.war file http://mydas.googlecode.com/svn/repository/uk/ac/ebi/mydas/template/MyDasTemplate/1.6.1/MyDasTemplate-1.6.1.war once downloaded you will need to unzip it. For mac I go to the file in finder and right click and select open with and select “stuffit” this application then unpacks the .war file in the directory the original file is in.

3) replace the person1.txt file with your own genotype data file (make sure there are no headers – just the data). The beginning of the file should look like this:

rs3094315 1 742429 AA
rs12562034 1 758311 GG
rs3934834 1 995669 CT

Where the columns are seperated by tabs and the colums represent the snp id, chromosome, position, genotype.

Make sure you rename your file to be the same as person1.txt

4) Edit the MydasServerConfig.xml file (you can use a normal text editor although an xml editor is better as it will highlight mistakes that are easily made). Go to the person1 data source (tip you can search for <datasource uri=”person1) then edit the query_uri urls replacing mychoiceofname with what you want (I recommend not using your name unless you the world to know what diseases you may be susceptible to etc…

so the query_uri for sources will look like this http://mychoiceofname.elasticbeanstalk.com/das/person1

5) repackage the MydasTemplate directory contents into a new .war file named as your substitution for mychoiceofname.

In unix like systems such as macosx you can cd to inside the directory MydasTemplate and run the follwing command:

jar cvf ../mychoiceofname.war *

6) To upload your application file (the .war file) Go to http://aws.amazon.com/ with your web browser and  use the “sign in to the console” button at the bottom right. The AWS console will look like this:

AWS console

AWS console

select “elastic benstalk” tab, “create new application” name it e.g. mychoiceofname click on the “choose file” button and select the .war file you have created earlier. Should look like this:

Application Details

Application Details

choose envirnoment name and ulr like so:

Environment

Environment

then press continue.

you can type in /das/sources for the application health check url like so:

Configuration Details

Configuration Details

click finish on the next screen that will look something like this:

Review

Review

wait a few minutes why the virtual machine and application are set up.

When the application icon is green you can test your das server by putting this url into a browser:

http://mychoiceofname.elasticbeanstalk.com/das/sources

to test your data source is working you can use this url:

http://mychoiceofname.elasticbeanstalk.com/das/person1/features?segment=1:742429,758311

assuming you have some snps in chromosome 1 in the region 742429,758311 you should see something like this in the output of the browser:

<?xml version="1.0" standalone="no"?>
<DASGFF>
  <GFF href="http://localhost:8080/das/person1/features?segment=1:742429,758311">
    <SEGMENT id="1" start="742429" stop="758311" total="43863" version="1.0" label="1">
      <FEATURE id="rs3094315" label="rs3094315">
        <TYPE id="AA" cvId="SO:0000694" category="SNP">SNP</TYPE>
        <METHOD id="experimental genomic evidence" cvId="ECO:0000073">experimental genomic evidence</METHOD>
        <START>742429</START>
        <END>742429</END>
      </FEATURE>
      <FEATURE id="rs12562034" label="rs12562034">
        <TYPE id="GG" cvId="SO:0000694" category="SNP">SNP</TYPE>
        <METHOD id="experimental genomic evidence" cvId="ECO:0000073">experimental genomic evidence</METHOD>
        <START>758311</START>
        <END>758311</END>
      </FEATURE>
    </SEGMENT>
  </GFF>
</DASGFF>

To view this data set in ensembl against the GRCh37 genome navigate to this url:
http://www.ensembl.org/Homo_sapiens/Location/View?db=core&r=1%3A742429-758311
click on "configure this page" at the top left. Choose "custom data" tab then the "attach das" link.
type your equivalent of "http://mychoiceofname.elasticbeanstalk.com/das/" into the "or other server" box. Type "person1" into the filter souces box. Click "next". Select the person1 using the tick box provided. Click "next". A message should come up saying

The following DAS sources have now been attached

click on the tick mark at the right hand corner.

A tack labelled “person1” should appear and boxes displayed if there are features present like so:

Genotype Features in Ensembl

Genotype Features in Ensembl


					
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