BioInstaller (version 0.3.7)

install.bioinfo: Download and install biology software or database

Description

Download and install biology software or database

Usage

install.bioinfo(name = c(), download.dir = c(), destdir = c(),
  name.saved = NULL, github.cfg = system.file("extdata",
  "config/github/github.toml", package = "BioInstaller"),
  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")), version = c(),
  local.source = NULL, show.all.versions = FALSE,
  show.all.names = FALSE, 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, license = "",
  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

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'

github.cfg

Configuration file of installed by github url, default is system.file('extdata', 'config/github/github.toml', package='BioInstaller')

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'))

version

Software version

local.source

Install from local source, github softwares need a cloned dir, and nongithub softwares can be installed from a compressed file (if it is a dir, you need set decompress to FALSE)

show.all.versions

Logical wheather show all avaliable versions can be install

show.all.names

Logical wheather show all avaliable names can be install

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

license

The BioInstaller download license code.

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 or a list

Examples

# NOT RUN {
db <- sprintf('%s/.BioInstaller', tempdir())
set.biosoftwares.db(db)
tryCatch(install.bioinfo('bwa', show.all.versions = TRUE), 
error = function(e) {
  message('Connecting Github failed. Please try it again later.')
})
unlink(db)
# }