Write Your Own Configuration File

Softwares and databases deposited on Github

Variables to control the download and installation steps of software and databases deposited on github:

• If you set use_git2r to false, BioInstaller will use the git of your system.
• If you set use_git2r to false and setted recursive_clone to true, BioInstaller will run this command git clone --recursive https://path/repo
• You can use the before_install stored the pre-installation steps
• The install mainly be used to store the installation steps. Besides, you can use your own installation script and setted it to #R# system('/path/yourscript')#R#
• The make_dir is the compile directory of software and database. Because the workdir of R default will be set to download.dir, and need be changed to make_dir finish install steps.
• All Bitbucket repo should set ‘bitbucket’ to ‘true’ (e.g. snakemake in github.toml)

[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 software version control can be done by git2r package and github tag API. Source URL of software or files deposited in github can be found by github_url in github.toml.

Softwares and databases of non-github

Variables to control the download and installation steps of software and databases not be deposited on github:

• github_url be replaced by source_url
• If you want to download multiple files in the source_url, you need to set url_all_download to true.
• rvest and RCurl packages can be used to parse the version information of software or databases of non-github.
• If you don’t want to use the built-in version reorder function, you need to set version_order_fixed to true. Optional, if the file count of source code was only one, you can set url_all_download to false and writing multiple URL. It will help you to avoid the invalid URL caused download fail.

[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 software and databases need a function parsing URL and use {{version}} to replace in the source_url.

Besides, BioInstaller uses configr glue to reduce the length of files name. It can help you to use less word to store more files name.

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)))}"
x <- read.config(blast.databases, glue.parse = TRUE)$db_blast_nr$source_url
length(x)
#> [1] 138
head(x)
#> [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"
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 /var/folders/nc/
#> yl5qhkkn6vxf_m7s_yz2kzvh0000gn/T//RtmpK8vw9W/filebbb14fb80eba 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"