install.bioinfo: Download and install biology software or database

In BioInstaller: Integrator of Bioinformatics Resources

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

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)

Example output

INFO [2019-12-04 10:05:22] Fetching bwa versions....
Featch the github version failed.
[1] "master"

BioInstaller documentation built on May 1, 2019, 11:17 p.m.