install.nongithub: Install or download softwares from non-Github Web site

In Miachol/BioInstaller: Integrator of Bioinformatics Resources

Install or download softwares from non-Github Web site

Description

Install or download softwares from non-Github Web site

Usage

install.nongithub(name = "", download.dir = NULL, destdir = NULL,
  version = NULL, local.source = NULL, show.all.versions = FALSE,
  name.saved = NULL, nongithub.cfg = c(system.file("extdata",
  "config/nongithub/nongithub.toml", package = "BioInstaller"),
  system.file("extdata", "config/db/db_main.toml", package =
  "BioInstaller"), system.file("extdata", "config/db/db_annovar.toml",
  package = "BioInstaller"), system.file("extdata",
  "config/db/db_blast.toml", package = "BioInstaller")),
  db = Sys.getenv("BIO_SOFTWARES_DB_ACTIVE", system.file("extdata",
  "demo/softwares_db_demo.yaml", package = "BioInstaller")),
  download.only = FALSE, decompress = TRUE, dependence.need = TRUE,
  showWarnings = FALSE, extra.list = list(), rcmd.parse = TRUE,
  bash.parse = TRUE, glue.parse = TRUE, glue.flag = "!!glue",
  save.to.db = TRUE, overwrite = FALSE, verbose = TRUE, ...)

Arguments

name	Software name
download.dir	A string, point the source code download destdir
destdir	A string, point the install path
version	Software version
local.source	Install from local source (a compressed file, if it is a dir, you need set decompress to FALSE)
show.all.versions	Logical wheather show all avaliable version can be install
name.saved	Software name when you want to install different version, you can use this to point the installed softwares name like 'GATK-3.7'
nongithub.cfg	Configuration file of installed by non github url, default is c(system.file('extdata', 'config/nongithub/nongithub.toml', package = 'BioInstaller'), system.file('extdata', 'config/db/db_main.toml', package = 'BioInstaller'), system.file('extdata', 'config/db/db_annovar.toml', package = 'BioInstaller'), system.file('extdata', 'config/db/db_blast.toml', package = 'BioInstaller'))
db	File of saving softwares infomation, default is Sys.getenv('BIO_SOFTWARES_DB_ACTIVE', system.file('extdata', 'demo/softwares_db_demo.yaml', package = 'BioInstaller'))
download.only	Logicol indicating wheather only download source or file (non-github)
decompress	Logicol indicating wheather need to decompress the downloaded file, default is TRUE
dependence.need	Logical should the dependence should be installed
showWarnings	Logical should the warnings on failure be shown?
extra.list	A list that can replace the configuration file 'debug' by list(debug = TRUE), and debug will be setted to TRUE
rcmd.parse	Logical wheather parse '@>@str_replace('abc', 'b', 'c')@<@' in config to 'acc'
bash.parse	Logical wheather parse '#>#echo $HOME#<#' in config to your HOME PATH
glue.parse	Logical wheather parse '!!glue1:5' in config to ['1','2','3','4','5']; ['nochange', '!!glue(1:5)', 'nochange'] => ['nochange', '1', '2', '3', '4', '5', 'nochange']
glue.flag	A character flage indicating wheater run glue() function to parse (Default is !!glue)
save.to.db	Ligical indicating wheather save the install infomation in db
overwrite	Force delete the destdir or download dir without a interactive message (careful)
verbose	Ligical indicating wheather show the log message
...	Other key and value paired need be saved in BioInstaller passed to change.info

Value

Bool Value

Examples

db <- sprintf('%s/.BioInstaller', tempdir())
set.biosoftwares.db(db)
## Not run: 
  install.nongithub('gmap', show.all.versions = TRUE)

## End(Not run)
unlink(db)

Miachol/BioInstaller documentation built on Feb. 1, 2023, 8:11 a.m.