introduction.rst

Introduction

What is Score?

Score facilitates the transfer and storage of your data seamlessly for cloud-based projects. File bundling, resumable downloads, and BAM/CRAM slicing make data transfer fast and smooth.

The method with which Score facilitates the transfer of data is through the use of pre-signed URLs. As such, Score can be thought of as a broker between an object storage system and user authorization system, validating user access and generating signed URLs for object access.

Features

  • Multipart Uploads and Downloads (high performance transfers)
  • Support for AWS S3, Azure Storage, Google Cloud Storage
  • Slicing of BAM and CRAM files by genomic region
  • Client includes some samtools functionality such as viewing reads from a BAM
  • MD5 validation of uploads and downloads
  • ACL security using OAuth2 and scopes based on study codes
  • Integrates with the SONG metadata system for data book keeping and consistency
  • REST API with swagger docs

Projects Using Score

  1. Cancer Collaboratory - Toronto: https://storage.cancercollaboratory.org/swagger-ui.html
  2. AWS - Virginia: https://virginia.cloud.icgc.org/swagger-ui.html

Getting Started

Client

The Score Client is available to download as both a docker container or as a Java CLI application.

The docker container can be pulled from here:

docker pull overture/score

For the Java CLI, use the following steps:

wget -O score-client.tar.gz https://artifacts.oicr.on.ca/artifactory/dcc-release/bio/overture/score-client/[RELEASE]/score-client-[RELEASE]-dist.tar.gz

tar xvzf score-client.tar.gz

echo export PATH=$(pwd)/score-client-x.x.x/bin:$PATH >> ~/.bashrc

source ~/.bashrc

# you will then be able to use it by running the following command anywhere is the system
score-client

Server

To be Added…

License

Copyright (c) 2018. Ontario Institute for Cancer Research

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.