Basic environment for using aegis, bio, and stm* packages. This provides the required functions to bootstrap and interact with each package.
To install you need to bootstrap from github directly:
devtools::install_github( "jae0/aegis.env" )
or you can add the following into your Rprofile:
pkgsInstalled = .packages(all.available = TRUE)
if (!"aegis.env" %in% pkgsInstalled ) {
message( "The package, aegis.env is missing, please install")
message( "Install right now? (y/n):")
o = readline()
if (o=="y"){
if (!"devtools" %in% pkgsInstalled ) {
install.packages("devtools", dependencies=TRUE, ask=FALSE)
}
require( devtools)
install_github( "jae0/aegis.env")
}
}
Then, you need to have an Rprofile set up properly such as:
libPaths("~/R")
homedir = path.expand("~")
tmpdir = file.path( homedir, "tmp" )
work_root = file.path( homedir, "work" ) ### replace with correct path to work directory (local temporary storage)
code_root = file.path( homedir, "bio" ) ### replace with correct path to the parent directory of your git-projects
data_root = file.path( homedir, "bio.data" ) ### replace with correct path to your data
# store your passwords and login here and make sure they are secure
passwords = file.path( homedir, ".passwords" )
if (file.exists(passwords)) source( passwords )
require( aegis.env )
Thereafter, you can used the bootstrapped environment to install the other basic tools:
aegis.env::project.libraryInstall()
If you have a local git clone of the required packages, you can install with:
aegis.env::project.libraryInstall(local=TRUE)
For usage, examples can be found in https://github.com/jae0/aegis/tree/master/inst/scripts/.
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