Cancer Gene Trust

Documentation for this project can be found on [Read the Docs](http://knowledger.readthedocs.org/en/latest/).

The distributed data coordination center (ddcc) tool to connect to the Cancer Gene Trust is documented below.

Please be aware that this is a software experiment and still changing a lot.

Installation

1. Install IPFS from http://ipfs.io
2. Git clone this repo (Python2.7 should be installed on most machines these days)

Start a steward node

First initialize the local block chain, create an accound and define a password:

ddcc initGeth

Write the password to a file and secure it:

echo myPassword > ~/.ddccPwd chmod 600 ~/.ddccPwd

Now start the geth ethereum steward node:

ddcc startNode

Prepare the submission

1. Create a file with metadata that describes your VCF files. You can create a minimal one for a single VCF like this:

   echo '{"sample1" : {"vcf_filename" : "test1.vcf.gz"}}' >> mySubmission.json

   You can find a demo submission directory in ALL/.

Do the IPFS submission

Run a command like this:

ddcc submit mySubmission.json --email me@somewhere.com --institution 'University, State, Country' -name 'John Doe, MD'

E.g. to submit the demo directory:

ddcc submit ALL/ALL-US.json --email max@soe.ucsc.edu --institution 'UC Santa Cruz' -name 'Maximilian Haeussler'

The demo data are somatic mutations from the TARGET Cancer sequencing project, ALL=Acute Lymphoblastic Leukemia.

The output looks like this:

...
file hash: QmaV9Lme9VjjbYxaaACR7BNK5Xiae8otrRTu9Fhn3PJ7ZX
Submission info JSON written to ALL/ALL-US.json.submitted
Adding ALL/ALL-US.json.submitted to IPFS
Submission ID written to ALL/ALL-US.json.submissionId
IPFS submission OK. Submission ID is QmemBUVjsYonnibtq6Jxi8yuyxmyhEuRAZQaLbZfkv1K9X

A submission includes many files. Each file has a hash for its ID that is unique for its content, and the overall submission has a hash for its ID that is unique for its content, which includes the hashes of the files it contains. Hence doing the same submission again will also give you the same submission ID. Thus, you can always resubmit if you are not sure of the ID and any changes to any of the files contained in the submission will result in a different file ID and hence a different submission ID.

Note the "Submission ID". You will need it later for the block chain.

Add the submission ID to the block chain

Run this command to append the submission ID to the block chain:

ddcc register QmemBUVjsYonnibtq6Jxi8yuyxmyhEuRAZQaLbZfkv1K9X