Loading Data

• v0 (Genomic Data)
  • Loading from the same host
  • Loading from a different host
  • Example
  • Data Manipulation
• v1 (I2B2 Demodata)
  • Loading in the same host
  • Loading in a different host
  • Dummy Generation
  • Example

The current version offers two different loading alternatives: (v0) loading of clinical and genomic data based on MAF datasets; and (v1) loading of generic i2b2 data. Currently these two loaders support each one dataset:

• v0: a genomic dataset (tcga_cbio publicly available in cBioPortal)
• v1: the i2b2 demodata.

Future releases of this software will allow for other arbitrary data sources, given that they follow a specific structure (e.g. BAM format).

Pre-Requisites

First get the repository containing the MedCo loader software, which already contains some test data for you to work with. Not that you need git-lfs for those data to be retrieved with the repository.

$ cd ~
$ git clone -b v0.1.1 https://github.com/lca1/medco-loader.git

Building Application

To get the MedCo loader application, pull it with Docker:

docker pull medco/medco-loader:v0.1.1