Examples of Templet Configuration File

Templet configuration files in BioInstaller are important. All of softwares and databases source URL, install script and other information were stored in these configuration files.

Most of configuration files be parsed by configr. Compared with original configr package #R# R CMD #R# is a different point which can be used to mark those R format command.

github.toml and nongithub.toml

Built-in configuration files: github.toml and nongithub.toml can be used to download and install several software and database. install.bioinfo(show.all.names = TRUE) can be used to get all of avaliable softwares and databases existed in github.toml and nongithub.toml.

Github Softwares

Some of item in github configuration file can be used to control the BioInstaller behavior:

use_git2r be setted to false, BioInstaller will use the git of your system.
use_git2r be setted to false and recursive_clone be setted to true, BioInstaller will do that git clone --recursive https://path/repo
before_install can be used to finish some pre-process step
install is the mainly item to control the install step. Moreover, you can use your install script saved in a file and run it by #R# system('/path/yourscript')#R#
make_dir is the compile directory of softwares which depend on your install script, workdir of R default be setted to download.dir and will be changed to make_dir when running install step.
bin_dir will be saved when finish install step

[bwa]
github_url = "https://github.com/lh3/bwa"
after_failure = "echo 'fail!'"
after_success = "echo 'successful!'"
make_dir = ["./"]
bin_dir = ["./"]

[bwa.before_install]
linux = ""
mac = ""

[bwa.install]
linux = "make"
mac = "make"

Github softwares version control can be done by git2r package and github tag API. Source url of softwares or files deposited in github can be found by github_url in github.toml.

Non-Github Softwares or Databases

Configuration file of non-github softwares and databases are similar to githubs: - github_url be replaced by source_url - url_all_download be setted to true if you want to download mulitple files. - rvest and RCurl packages can be used to parse the version infomation of non-github softwares or databases. - version_order_fixed can be setted to true if you don’t want to use the built-in version reorder function. If you set url_all_download to false, which can let us using multiple mirror to avoid one of invalid URL.

[gmap]
# {{version}} will be parsed to your install.bioinfo `version` parameter
# or the newest version parsed from fetched data.
source_url = "http://research-pub.gene.com/gmap/src/{{version}}.tar.gz"
after_failure = "echo 'fail!'"
after_success = "echo 'successful!'"
make_dir = ["./"]
bin_dir = ["./"]

[gmap.before_install]
linux = ""
mac = ""

[gmap.install]
linux = "./configure --prefix=`pwd` && make && make install"
mac = ["sed -i s/\"## CFLAGS='-O3 -m64' .*\"/\"CFLAGS='-O3 -m64'\"/ config.site",
"./configure --prefix=`pwd` && make && make install"]

Version control of non-github softwares and databases need a function parsing URL and use {{version}} to replace in the source_url.

nongithub_databases_blast.toml

This configuration file can be used to download NCBI blast database: install.bioinfo(nongithub.cfg = system.file('extdata', 'databases/blast.toml', package = 'BioInstaller'), show.all.names = TRUE).

BioInstaller use configr glue to reduce the length of files name. That using less word to storage more files name. More useful databases FTP url can be accessed in the future. I hope you can set your own configuration file not only use the BioInstaller built-in configuration files.

library(configr)
library(BioInstaller)
blast.databases <- system.file('extdata', 
  'config/db/db_blast.toml', package = 'BioInstaller')

read.config(blast.databases)$db_blast_nr$source_url
#> [1] "!!glue ftp://ftp.ncbi.nih.gov/blast/db/nr.{ids=sprintf('%02d', 0:68);rep(ids, 2)}.tar.gz{c(rep('', length(ids)), rep('.md5', length(ids)))}"
read.config(blast.databases, glue.parse = TRUE)$db_blast_nr$source_url
#>   [1] "ftp://ftp.ncbi.nih.gov/blast/db/nr.00.tar.gz"    
#>   [2] "ftp://ftp.ncbi.nih.gov/blast/db/nr.01.tar.gz"    
#>   [3] "ftp://ftp.ncbi.nih.gov/blast/db/nr.02.tar.gz"    
#>   [4] "ftp://ftp.ncbi.nih.gov/blast/db/nr.03.tar.gz"    
#>   [5] "ftp://ftp.ncbi.nih.gov/blast/db/nr.04.tar.gz"    
#>   [6] "ftp://ftp.ncbi.nih.gov/blast/db/nr.05.tar.gz"    
#>   [7] "ftp://ftp.ncbi.nih.gov/blast/db/nr.06.tar.gz"    
#>   [8] "ftp://ftp.ncbi.nih.gov/blast/db/nr.07.tar.gz"    
#>   [9] "ftp://ftp.ncbi.nih.gov/blast/db/nr.08.tar.gz"    
#>  [10] "ftp://ftp.ncbi.nih.gov/blast/db/nr.09.tar.gz"    
#>  [11] "ftp://ftp.ncbi.nih.gov/blast/db/nr.10.tar.gz"    
#>  [12] "ftp://ftp.ncbi.nih.gov/blast/db/nr.11.tar.gz"    
#>  [13] "ftp://ftp.ncbi.nih.gov/blast/db/nr.12.tar.gz"    
#>  [14] "ftp://ftp.ncbi.nih.gov/blast/db/nr.13.tar.gz"    
#>  [15] "ftp://ftp.ncbi.nih.gov/blast/db/nr.14.tar.gz"    
#>  [16] "ftp://ftp.ncbi.nih.gov/blast/db/nr.15.tar.gz"    
#>  [17] "ftp://ftp.ncbi.nih.gov/blast/db/nr.16.tar.gz"    
#>  [18] "ftp://ftp.ncbi.nih.gov/blast/db/nr.17.tar.gz"    
#>  [19] "ftp://ftp.ncbi.nih.gov/blast/db/nr.18.tar.gz"    
#>  [20] "ftp://ftp.ncbi.nih.gov/blast/db/nr.19.tar.gz"    
#>  [21] "ftp://ftp.ncbi.nih.gov/blast/db/nr.20.tar.gz"    
#>  [22] "ftp://ftp.ncbi.nih.gov/blast/db/nr.21.tar.gz"    
#>  [23] "ftp://ftp.ncbi.nih.gov/blast/db/nr.22.tar.gz"    
#>  [24] "ftp://ftp.ncbi.nih.gov/blast/db/nr.23.tar.gz"    
#>  [25] "ftp://ftp.ncbi.nih.gov/blast/db/nr.24.tar.gz"    
#>  [26] "ftp://ftp.ncbi.nih.gov/blast/db/nr.25.tar.gz"    
#>  [27] "ftp://ftp.ncbi.nih.gov/blast/db/nr.26.tar.gz"    
#>  [28] "ftp://ftp.ncbi.nih.gov/blast/db/nr.27.tar.gz"    
#>  [29] "ftp://ftp.ncbi.nih.gov/blast/db/nr.28.tar.gz"    
#>  [30] "ftp://ftp.ncbi.nih.gov/blast/db/nr.29.tar.gz"    
#>  [31] "ftp://ftp.ncbi.nih.gov/blast/db/nr.30.tar.gz"    
#>  [32] "ftp://ftp.ncbi.nih.gov/blast/db/nr.31.tar.gz"    
#>  [33] "ftp://ftp.ncbi.nih.gov/blast/db/nr.32.tar.gz"    
#>  [34] "ftp://ftp.ncbi.nih.gov/blast/db/nr.33.tar.gz"    
#>  [35] "ftp://ftp.ncbi.nih.gov/blast/db/nr.34.tar.gz"    
#>  [36] "ftp://ftp.ncbi.nih.gov/blast/db/nr.35.tar.gz"    
#>  [37] "ftp://ftp.ncbi.nih.gov/blast/db/nr.36.tar.gz"    
#>  [38] "ftp://ftp.ncbi.nih.gov/blast/db/nr.37.tar.gz"    
#>  [39] "ftp://ftp.ncbi.nih.gov/blast/db/nr.38.tar.gz"    
#>  [40] "ftp://ftp.ncbi.nih.gov/blast/db/nr.39.tar.gz"    
#>  [41] "ftp://ftp.ncbi.nih.gov/blast/db/nr.40.tar.gz"    
#>  [42] "ftp://ftp.ncbi.nih.gov/blast/db/nr.41.tar.gz"    
#>  [43] "ftp://ftp.ncbi.nih.gov/blast/db/nr.42.tar.gz"    
#>  [44] "ftp://ftp.ncbi.nih.gov/blast/db/nr.43.tar.gz"    
#>  [45] "ftp://ftp.ncbi.nih.gov/blast/db/nr.44.tar.gz"    
#>  [46] "ftp://ftp.ncbi.nih.gov/blast/db/nr.45.tar.gz"    
#>  [47] "ftp://ftp.ncbi.nih.gov/blast/db/nr.46.tar.gz"    
#>  [48] "ftp://ftp.ncbi.nih.gov/blast/db/nr.47.tar.gz"    
#>  [49] "ftp://ftp.ncbi.nih.gov/blast/db/nr.48.tar.gz"    
#>  [50] "ftp://ftp.ncbi.nih.gov/blast/db/nr.49.tar.gz"    
#>  [51] "ftp://ftp.ncbi.nih.gov/blast/db/nr.50.tar.gz"    
#>  [52] "ftp://ftp.ncbi.nih.gov/blast/db/nr.51.tar.gz"    
#>  [53] "ftp://ftp.ncbi.nih.gov/blast/db/nr.52.tar.gz"    
#>  [54] "ftp://ftp.ncbi.nih.gov/blast/db/nr.53.tar.gz"    
#>  [55] "ftp://ftp.ncbi.nih.gov/blast/db/nr.54.tar.gz"    
#>  [56] "ftp://ftp.ncbi.nih.gov/blast/db/nr.55.tar.gz"    
#>  [57] "ftp://ftp.ncbi.nih.gov/blast/db/nr.56.tar.gz"    
#>  [58] "ftp://ftp.ncbi.nih.gov/blast/db/nr.57.tar.gz"    
#>  [59] "ftp://ftp.ncbi.nih.gov/blast/db/nr.58.tar.gz"    
#>  [60] "ftp://ftp.ncbi.nih.gov/blast/db/nr.59.tar.gz"    
#>  [61] "ftp://ftp.ncbi.nih.gov/blast/db/nr.60.tar.gz"    
#>  [62] "ftp://ftp.ncbi.nih.gov/blast/db/nr.61.tar.gz"    
#>  [63] "ftp://ftp.ncbi.nih.gov/blast/db/nr.62.tar.gz"    
#>  [64] "ftp://ftp.ncbi.nih.gov/blast/db/nr.63.tar.gz"    
#>  [65] "ftp://ftp.ncbi.nih.gov/blast/db/nr.64.tar.gz"    
#>  [66] "ftp://ftp.ncbi.nih.gov/blast/db/nr.65.tar.gz"    
#>  [67] "ftp://ftp.ncbi.nih.gov/blast/db/nr.66.tar.gz"    
#>  [68] "ftp://ftp.ncbi.nih.gov/blast/db/nr.67.tar.gz"    
#>  [69] "ftp://ftp.ncbi.nih.gov/blast/db/nr.68.tar.gz"    
#>  [70] "ftp://ftp.ncbi.nih.gov/blast/db/nr.00.tar.gz.md5"
#>  [71] "ftp://ftp.ncbi.nih.gov/blast/db/nr.01.tar.gz.md5"
#>  [72] "ftp://ftp.ncbi.nih.gov/blast/db/nr.02.tar.gz.md5"
#>  [73] "ftp://ftp.ncbi.nih.gov/blast/db/nr.03.tar.gz.md5"
#>  [74] "ftp://ftp.ncbi.nih.gov/blast/db/nr.04.tar.gz.md5"
#>  [75] "ftp://ftp.ncbi.nih.gov/blast/db/nr.05.tar.gz.md5"
#>  [76] "ftp://ftp.ncbi.nih.gov/blast/db/nr.06.tar.gz.md5"
#>  [77] "ftp://ftp.ncbi.nih.gov/blast/db/nr.07.tar.gz.md5"
#>  [78] "ftp://ftp.ncbi.nih.gov/blast/db/nr.08.tar.gz.md5"
#>  [79] "ftp://ftp.ncbi.nih.gov/blast/db/nr.09.tar.gz.md5"
#>  [80] "ftp://ftp.ncbi.nih.gov/blast/db/nr.10.tar.gz.md5"
#>  [81] "ftp://ftp.ncbi.nih.gov/blast/db/nr.11.tar.gz.md5"
#>  [82] "ftp://ftp.ncbi.nih.gov/blast/db/nr.12.tar.gz.md5"
#>  [83] "ftp://ftp.ncbi.nih.gov/blast/db/nr.13.tar.gz.md5"
#>  [84] "ftp://ftp.ncbi.nih.gov/blast/db/nr.14.tar.gz.md5"
#>  [85] "ftp://ftp.ncbi.nih.gov/blast/db/nr.15.tar.gz.md5"
#>  [86] "ftp://ftp.ncbi.nih.gov/blast/db/nr.16.tar.gz.md5"
#>  [87] "ftp://ftp.ncbi.nih.gov/blast/db/nr.17.tar.gz.md5"
#>  [88] "ftp://ftp.ncbi.nih.gov/blast/db/nr.18.tar.gz.md5"
#>  [89] "ftp://ftp.ncbi.nih.gov/blast/db/nr.19.tar.gz.md5"
#>  [90] "ftp://ftp.ncbi.nih.gov/blast/db/nr.20.tar.gz.md5"
#>  [91] "ftp://ftp.ncbi.nih.gov/blast/db/nr.21.tar.gz.md5"
#>  [92] "ftp://ftp.ncbi.nih.gov/blast/db/nr.22.tar.gz.md5"
#>  [93] "ftp://ftp.ncbi.nih.gov/blast/db/nr.23.tar.gz.md5"
#>  [94] "ftp://ftp.ncbi.nih.gov/blast/db/nr.24.tar.gz.md5"
#>  [95] "ftp://ftp.ncbi.nih.gov/blast/db/nr.25.tar.gz.md5"
#>  [96] "ftp://ftp.ncbi.nih.gov/blast/db/nr.26.tar.gz.md5"
#>  [97] "ftp://ftp.ncbi.nih.gov/blast/db/nr.27.tar.gz.md5"
#>  [98] "ftp://ftp.ncbi.nih.gov/blast/db/nr.28.tar.gz.md5"
#>  [99] "ftp://ftp.ncbi.nih.gov/blast/db/nr.29.tar.gz.md5"
#> [100] "ftp://ftp.ncbi.nih.gov/blast/db/nr.30.tar.gz.md5"
#> [101] "ftp://ftp.ncbi.nih.gov/blast/db/nr.31.tar.gz.md5"
#> [102] "ftp://ftp.ncbi.nih.gov/blast/db/nr.32.tar.gz.md5"
#> [103] "ftp://ftp.ncbi.nih.gov/blast/db/nr.33.tar.gz.md5"
#> [104] "ftp://ftp.ncbi.nih.gov/blast/db/nr.34.tar.gz.md5"
#> [105] "ftp://ftp.ncbi.nih.gov/blast/db/nr.35.tar.gz.md5"
#> [106] "ftp://ftp.ncbi.nih.gov/blast/db/nr.36.tar.gz.md5"
#> [107] "ftp://ftp.ncbi.nih.gov/blast/db/nr.37.tar.gz.md5"
#> [108] "ftp://ftp.ncbi.nih.gov/blast/db/nr.38.tar.gz.md5"
#> [109] "ftp://ftp.ncbi.nih.gov/blast/db/nr.39.tar.gz.md5"
#> [110] "ftp://ftp.ncbi.nih.gov/blast/db/nr.40.tar.gz.md5"
#> [111] "ftp://ftp.ncbi.nih.gov/blast/db/nr.41.tar.gz.md5"
#> [112] "ftp://ftp.ncbi.nih.gov/blast/db/nr.42.tar.gz.md5"
#> [113] "ftp://ftp.ncbi.nih.gov/blast/db/nr.43.tar.gz.md5"
#> [114] "ftp://ftp.ncbi.nih.gov/blast/db/nr.44.tar.gz.md5"
#> [115] "ftp://ftp.ncbi.nih.gov/blast/db/nr.45.tar.gz.md5"
#> [116] "ftp://ftp.ncbi.nih.gov/blast/db/nr.46.tar.gz.md5"
#> [117] "ftp://ftp.ncbi.nih.gov/blast/db/nr.47.tar.gz.md5"
#> [118] "ftp://ftp.ncbi.nih.gov/blast/db/nr.48.tar.gz.md5"
#> [119] "ftp://ftp.ncbi.nih.gov/blast/db/nr.49.tar.gz.md5"
#> [120] "ftp://ftp.ncbi.nih.gov/blast/db/nr.50.tar.gz.md5"
#> [121] "ftp://ftp.ncbi.nih.gov/blast/db/nr.51.tar.gz.md5"
#> [122] "ftp://ftp.ncbi.nih.gov/blast/db/nr.52.tar.gz.md5"
#> [123] "ftp://ftp.ncbi.nih.gov/blast/db/nr.53.tar.gz.md5"
#> [124] "ftp://ftp.ncbi.nih.gov/blast/db/nr.54.tar.gz.md5"
#> [125] "ftp://ftp.ncbi.nih.gov/blast/db/nr.55.tar.gz.md5"
#> [126] "ftp://ftp.ncbi.nih.gov/blast/db/nr.56.tar.gz.md5"
#> [127] "ftp://ftp.ncbi.nih.gov/blast/db/nr.57.tar.gz.md5"
#> [128] "ftp://ftp.ncbi.nih.gov/blast/db/nr.58.tar.gz.md5"
#> [129] "ftp://ftp.ncbi.nih.gov/blast/db/nr.59.tar.gz.md5"
#> [130] "ftp://ftp.ncbi.nih.gov/blast/db/nr.60.tar.gz.md5"
#> [131] "ftp://ftp.ncbi.nih.gov/blast/db/nr.61.tar.gz.md5"
#> [132] "ftp://ftp.ncbi.nih.gov/blast/db/nr.62.tar.gz.md5"
#> [133] "ftp://ftp.ncbi.nih.gov/blast/db/nr.63.tar.gz.md5"
#> [134] "ftp://ftp.ncbi.nih.gov/blast/db/nr.64.tar.gz.md5"
#> [135] "ftp://ftp.ncbi.nih.gov/blast/db/nr.65.tar.gz.md5"
#> [136] "ftp://ftp.ncbi.nih.gov/blast/db/nr.66.tar.gz.md5"
#> [137] "ftp://ftp.ncbi.nih.gov/blast/db/nr.67.tar.gz.md5"
#> [138] "ftp://ftp.ncbi.nih.gov/blast/db/nr.68.tar.gz.md5"
mask.github <- tempfile()
file.create(mask.github)
#> [1] TRUE
install.bioinfo(nongithub.cfg = blast.databases, github.cfg = mask.github,
  show.all.names = TRUE)
#> Warning in fetch.config(github.cfg): Configuration file /tmp/RtmpWodq64/
#> file951d7d03c91b is empty, please check the links.
#>  [1] "db_blast_env_nr"                  "db_blast_est_human"              
#>  [3] "db_blast_est_mouse"               "db_blast_est_others"             
#>  [5] "db_blast_gss"                     "db_blast_htgs"                   
#>  [7] "db_blast_human_genomic"           "db_blast_landmark"               
#>  [9] "db_blast_mouse_genomic"           "db_blast_nr"                     
#> [11] "db_blast_nt"                      "db_blast_other_genomic"          
#> [13] "db_blast_pataa"                   "db_blast_patnt"                  
#> [15] "db_blast_pdbaa"                   "db_blast_pdbnt"                  
#> [17] "db_blast_ref_prok_rep_genomes"    "db_blast_ref_viroids_rep_genomes"
#> [19] "db_blast_ref_viruses_rep_genomes" "db_blast_refseq_genomic"         
#> [21] "db_blast_refseq_protein"          "db_blast_refseq_rna"             
#> [23] "db_blast_refseqgene"              "db_blast_sts"                    
#> [25] "db_blast_swissprot"               "db_blast_taxdb"                  
#> [27] "db_blast_tsa_nr"                  "db_blast_tsa_nt"                 
#> [29] "db_blast_vector"

Automatic parse from BIO_SOFTWARES_DB_ACTIVE database

To resolve the dependence and its path, BioInstall can automatic recogniztion the {{key:value}} format expression and get its real value from BioInstall BIO_SOFWARES_DB_ACTIVE database which were be setted by environment variable BIO_SOFTWARES_DB_ACTIVE and parameter db.

For example, Pindel need the htslib to finish its install, and we use ./INSTALL {{htslib:source.dir}} as the install step of Pindel that the value be setted in system.file("extdata", "github.toml", package = "BioInstaller") file Pindel section. In R, the {{htslib:source.dir}} will be replaced by the value that were stored in BIO_SOFTWARES_DB_ACTIVE or db, a parameter of install.bioinfo function, which indicating the BioInstall Database PATH. More example can be founded in configr parse.extra ‘other.config’ parameter.

Automatic parse from install.bioinfo parameter extra.list

To improve the flexibility of configuration templet, BioInstall can automatic recogniztion the {{parameters}} format expression and get its value if its existed in install.bioinfo extra.list parameter and name, version, os.version, destdir were default be setted.

For example, GMAP source_url need to point the version value, and we use source_url = "http://research-pub.gene.com/gmap/src/{{version}}.tar.gz" as the download URL and can be used to install different version GMAP that the value be setted in system.file("extdata", "nongithub.toml", package = "BioInstaller") file gmap section. In R, the {{version}} will be replaced by the version parameter value of install.bioinfo (if version were NULL, it will be setted to be the newst version). More example can be founded in configr parse.extra ‘extra.list’ parameter.