README

To build a command, simply use exec. The first argument is the command name, and you can also provide the full path. After that, pass the command parameters. This will create a command object:

exec("echo", "$PATH")
#> <Command: echo>

Sys.setenv(TEST = "blit is awesome")
exec("echo", "$TEST") |> cmd_run()
#> Running command: /usr/bin/echo $TEST
#> 
#> blit is awesome
Sys.unsetenv("TEST")

Several functions allow you to control the environment when running the command:

exec("echo", "$TEST") |>
    cmd_envvar(TEST = "blit is very awesome") |>
    cmd_run()
#> Setting environment variables: TEST
#> Running command: /usr/bin/echo $TEST
#> 
#> blit is very awesome

python() |> cmd_help()
#> Running command: /usr/bin/python3 --help
#> 
#> usage: /usr/bin/python3 [option] ... [-c cmd | -m mod | file | -] [arg] ...
#> Options (and corresponding environment variables):
#> -b     : issue warnings about converting bytes/bytearray to str and comparing
#>          bytes/bytearray with str or bytes with int. (-bb: issue errors)
#> -B     : don't write .pyc files on import; also PYTHONDONTWRITEBYTECODE=x
#> -c cmd : program passed in as string (terminates option list)
#> -d     : turn on parser debugging output (for experts only, only works on
#>          debug builds); also PYTHONDEBUG=x
#> -E     : ignore PYTHON* environment variables (such as PYTHONPATH)
#> -h     : print this help message and exit (also -? or --help)
#> -i     : inspect interactively after running script; forces a prompt even
#>          if stdin does not appear to be a terminal; also PYTHONINSPECT=x
#> -I     : isolate Python from the user's environment (implies -E and -s)
#> -m mod : run library module as a script (terminates option list)
#> -O     : remove assert and __debug__-dependent statements; add .opt-1 before
#>          .pyc extension; also PYTHONOPTIMIZE=x
#> -OO    : do -O changes and also discard docstrings; add .opt-2 before
#>          .pyc extension
#> -P     : don't prepend a potentially unsafe path to sys.path; also
#>          PYTHONSAFEPATH
#> -q     : don't print version and copyright messages on interactive startup
#> -s     : don't add user site directory to sys.path; also PYTHONNOUSERSITE=x
#> -S     : don't imply 'import site' on initialization
#> -u     : force the stdout and stderr streams to be unbuffered;
#>          this option has no effect on stdin; also PYTHONUNBUFFERED=x
#> -v     : verbose (trace import statements); also PYTHONVERBOSE=x
#>          can be supplied multiple times to increase verbosity
#> -V     : print the Python version number and exit (also --version)
#>          when given twice, print more information about the build
#> -W arg : warning control; arg is action:message:category:module:lineno
#>          also PYTHONWARNINGS=arg
#> -x     : skip first line of source, allowing use of non-Unix forms of #!cmd
#> -X opt : set implementation-specific option
#> --check-hash-based-pycs always|default|never:
#>          control how Python invalidates hash-based .pyc files
#> --help-env: print help about Python environment variables and exit
#> --help-xoptions: print help about implementation-specific -X options and exit
#> --help-all: print complete help information and exit
#> 
#> Arguments:
#> file   : program read from script file
#> -      : program read from stdin (default; interactive mode if a tty)
#> arg ...: arguments passed to program in sys.argv[1:]

perl() |> cmd_help()
#> Running command: /usr/bin/perl --help
#> 
#> 
#> Usage: /usr/bin/perl [switches] [--] [programfile] [arguments]
#>   -0[octal/hexadecimal] specify record separator (\0, if no argument)
#>   -a                    autosplit mode with -n or -p (splits $_ into @F)
#>   -C[number/list]       enables the listed Unicode features
#>   -c                    check syntax only (runs BEGIN and CHECK blocks)
#>   -d[t][:MOD]           run program under debugger or module Devel::MOD
#>   -D[number/letters]    set debugging flags (argument is a bit mask or alphabets)
#>   -e commandline        one line of program (several -e's allowed, omit programfile)
#>   -E commandline        like -e, but enables all optional features
#>   -f                    don't do $sitelib/sitecustomize.pl at startup
#>   -F/pattern/           split() pattern for -a switch (//'s are optional)
#>   -g                    read all input in one go (slurp), rather than line-by-line (alias for -0777)
#>   -i[extension]         edit <> files in place (makes backup if extension supplied)
#>   -Idirectory           specify @INC/#include directory (several -I's allowed)
#>   -l[octnum]            enable line ending processing, specifies line terminator
#>   -[mM][-]module        execute "use/no module..." before executing program
#>   -n                    assume "while (<>) { ... }" loop around program
#>   -p                    assume loop like -n but print line also, like sed
#>   -s                    enable rudimentary parsing for switches after programfile
#>   -S                    look for programfile using PATH environment variable
#>   -t                    enable tainting warnings
#>   -T                    enable tainting checks
#>   -u                    dump core after parsing program
#>   -U                    allow unsafe operations
#>   -v                    print version, patchlevel and license
#>   -V[:configvar]        print configuration summary (or a single Config.pm variable)
#>   -w                    enable many useful warnings
#>   -W                    enable all warnings
#>   -x[directory]         ignore text before #!perl line (optionally cd to directory)
#>   -X                    disable all warnings
#>   
#> Run 'perldoc perl' for more help with Perl.

One of the great features of blit is its ability to translate the R pipe (%>% or |>) into the Linux pipe (|). All functions used to create a command object can accept another command object. The internal will capture the first unnamed input value. If it is a command object, it will be removed from the call and saved. When the command object is run, the saved command will be passed through the pipe (|) to the command.

tmpdir <- tempdir()
file <- tempfile(tmpdir = tmpdir)
writeLines(letters, con = file)
file2 <- tempfile()
exec("gzip", "-c", file) |>
    exec("gzip", "-d", ">", file2) |>
    cmd_run()
#> Running command: /usr/bin/gzip -c /tmp/RtmpxPWVpK/file250bb31a59d402 |
#> /usr/bin/gzip -d > /tmp/RtmpxPWVpK/file250bb36ba42f5b
identical(readLines(file), readLines(file2))
#> [1] TRUE

file.remove(file)
#> [1] TRUE
file.remove(file2)
#> [1] TRUE

Session Informations

sessionInfo()
#> R version 4.4.2 (2024-10-31)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#> 
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so;  LAPACK version 3.8.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: Asia/Shanghai
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] blit_0.1.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] compiler_4.4.2    R6_2.5.1          fastmap_1.2.0     cli_3.6.3        
#>  [5] tools_4.4.2       htmltools_0.5.8.1 withr_3.0.2       yaml_2.3.10      
#>  [9] rmarkdown_2.29    knitr_1.49        xfun_0.49         digest_0.6.37    
#> [13] rlang_1.1.4       sys_3.4.3         evaluate_1.0.1

blit: Bioinformatics Library for Integrated Tools

Installation

Example

Session Informations