install.nongithub: Install or download softwares from non-Github Web site
In BioInstaller: Integrator of Bioinformatics Resources

Description Usage Arguments Value Examples

Install or download softwares from non-Github Web site

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, ...)

`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`

Bool Value

db <- sprintf('%s/.BioInstaller', tempdir())
set.biosoftwares.db(db)
tryCatch(install.nongithub('gmap', show.all.versions = TRUE),
error = function(e) {
  message('Connecting Gmap website failed. Please try it again later.')
})
unlink(db)