opencgaR 1.4.0
OpenCGA is an open-source project that aims to provide a Big Data storage engine and analysis framework for genomic scale data analysis of hundreds of terabytes or even petabytes. For users, its main features include uploading and downloading files to a repository, storing their information in a generic way (non-dependant of the original file-format) and retrieving this information efficiently. For developers, it will be a platform for supporting the most used bioinformatics file formats and accelerating the development of visualization and analysis applications.
The OpencgaR client provides a user-friendly interface to work with OpenCGA REST Web Services through R and has been implemented following the Bioconductor guidelines for package development which promote high-quality, well documented and interoperable software. The source code of the R package can be found in GitHub. For more information see the documentation website.
Please visit http://docs.opencb.org/display/opencga/Installation+Guide for detailed information on how to install and configure OpenCGA.
A set of methods have been implemented to deal with the connectivity and login to the REST host. Connection to the host is done in two steps using the functions initOpencgaR and opencgaLogin for defining the connection details and loging in, respectively.
The initOpencgaR function accepts either host and version information or a configuration file (as list() or in YAML or JSON format). The opencgaLogin function stablishes the connection with the host. It requires an object opencgaR (created using initOpencgaR) and the login details: user and password. User and password can be introduced interactively through a popup window using interactive=TRUE, to avoid typing user credentials in the R script.
The code below shows the different ways to initialise the OpenCGA connection with the REST server.
# Initialise connection specifying host and REST version
con <- initOpencgaR(host = "http://localhost:8080/opencga/", version = "v1")
# Initialise connection using configuration (list)
conf <- list(version="v1", rest=list(host="http://localhost:8080/opencga/"))
con <- initOpencgaR(opencgaConfig=conf)
# Initialise connection using configuration (YAML or JSON format)
conf <- "/path/to/conf/client-configuration.yml"
con <- initOpencgaR(opencgaConfig=conf)Once the connection has been initialised users can login specifying their OpenCGA user ID and password.
# Log in
con <- opencgaLogin(opencga = con, userid = "user", passwd = "pass")