GeneHive R package

Getting started

1. Set environment variables

When the GeneHive package is loaded, several R session options are set based on the following environment variables:

• HIVE_USERNAME The user name to be used to connect to the GeneHive instance. If not specified, Sys.info()["user"] will be used.
• HIVE_HOSTNAME The name of the GeneHive server. If not specified, "localhost" will be used.
• HIVE_HTTPS Set to true for HTTPS traffic or false for HTTP traffic. If not specified, HTTPS traffic will be used.

In a Unix-like system (including Macs), these may be set with the export command.

For example, the following lines might be added to a ~/.bashrc file:

# GeneHive environment variables
export HIVE_USERNAME="agower"
export HIVE_HOSTNAME="genehive.bu.edu"
export HIVE_HTTPS=true

In a Windows environment, these may be set through the Environment Variables system dialog (accessible by searching the Control Panel or Start menu).

2. Install the uuidtools and GeneHive packages

The GeneHive package and its dependency uuidtools may be installed directly from GitHub with the commands:

devtools::install_github("agower/uuidtools")
devtools::install_github("agower/GeneHive")

3. Change the password

You will receive a temporary password from the administrator of the GeneHive instance when your account is created.

You should replace this password with a strong, random password using the commands:

library(GeneHive)
changePassword()

By default, the changePassword() function performs the following actions:

• Generate a random, strong password, using /dev/urandom (if available) or the R random number generator otherwise
• Add the current hostname, username, and random password to ~/.netrc (in Unix-like systems) or ~/_netrc (in Windows).

The .netrc file format is simple: each line contains a separate whitespace-delimited entry describing a machine, username, and password. For example, a typical entry might look like:

machine genehive.bu.edu login agower password Fbyd0+TQFPLjuGEU_4vd

4. Test the credentials

The simplest way to test whether a connection can be made to a GeneHive is to issue a command to list all visible users. As this will always include at least the user performing the query, it should always return a result, regardless of the state of the hive, and is therefore a useful quick check for connectivity.

For example:

> listUsers()
  username     group    groups superuser         email firstName lastName  ...  active
1   agower rootgroup rootgroup      TRUE [email protected]      Adam    Gower         TRUE