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