init_gmql: Init GMQL server

In DEIB-GECO/RGMQL: GenoMetric Query Language for R/Bioconductor

Init GMQL server

Description

It initializes and runs GMQL server for executing GMQL query. It also performs a login to GMQL REST services suite, if needed

Usage

init_gmql(
  output_format = "GTF",
  remote_processing = FALSE,
  url = NULL,
  username = NULL,
  password = NULL
)

Arguments

output_format	string that identifies the output format of all sample files. It can be TAB, GTF or COLLECT: TAB: tab-delimited file format GTF: tab-delimited text standard format based on the General Feature Format COLLECT: used for storing output in memory (only in the case of local processing, i.e., remote_processing = FALSE)
remote_processing	logical value specifying the processing mode. True for processing on cluster (remote), false for local processing.
url	string url of server: It must contain the server address and base url; service name is added automatically. If NULL, no login is performed. You can always perform it by calling the function login_gmql explicitly
username	string name used during remote server signup
password	string password used during remote server signup

Value

None

Examples

## This statement initializes GMQL with local processing with sample files 
## output format as tab-delimited

init_gmql("tab", FALSE)

## This statement initializes GMQL with remote processing

remote_url = "http://www.gmql.eu/gmql-rest/"
init_gmql(remote_processing = TRUE, url = remote_url)

DEIB-GECO/RGMQL documentation built on Feb. 17, 2024, 10:39 p.m.