rush -- a cross-platform command-line tool for executing jobs in parallel

rush is a tool similar to GNU parallel and gargs. rush borrows some idea from them and has some unique features, e.g., supporting custom defined variables, resuming multi-line commands, more advanced embeded replacement strings.

These features make rush suitable for easily and flexibly parallelizing complex workflows in fields like Bioinformatics (see examples).

Table of Contents

• Features
• Performance
• Installation
• Usage
• Examples
• Special Cases
• Contributors
• Acknowledgements
• Contact
• License

Features

Major:

• Supporting Linux, OS X and Windows (not CygWin)!
• Avoid mixed line from multiple processes without loss of performance,

• Timeout (-t), terminating the timed-out command and its child-process tree. (--timeout in GNU parallel)
• Retry (-r). (--retry-failed --joblog in GNU parallel)
• Safe exit after capturing Ctrl-C: Linux uses native SIGINT/SIGKILL signals;

• Continue (-c). (--resume --joblog in GNU parallel,

• awk -v like custom defined variables (-v). (Using Shell variable in GNU parallel)
• Keeping output in order of input (-k). (Same -k/--keep-order in GNU parallel)
• Exit on first error (-e): stop scheduling and clean up active child processes. (--halt 2 in GNU parallel)
• Settable record delimiter (-D, default \n). (--recstart and --recend in GNU parallel)
• Settable records sending to every command (-n, default 1). (-n/--max-args in GNU parallel)
• Settable field delimiter (-d, default \s+). (Same -d/--delimiter in GNU parallel)
• Practical replacement strings (like GNU parallel):

• Preset variable (macro), e.g., rush -v p={^suffix} 'echo {p}_new_suffix',

Minor:

• Dry run (--dry-run). (Same in GNU parallel)
• Trim input data (--trim). (Same in GNU parallel)
• Verbose output (--verbose). (Same in GNU parallel)

Performance

Performance of rush is similar to gargs, and they are both slightly faster than parallel (Perl) and both slower than Rust parallel (discussion).

Note that speed is not the #.1 target, especially for processes that last long.

Installation

rush is implemented in Go programming language, executable binary files for most popular operating systems are freely available in release page.

Method 0: Conda

Install conda, then run

conda install -c conda-forge rush

Or use mamba, which is faster.

mamba install -c conda-forge rush

Method 1: Download binaries

rush v0.10.0

OS |Arch |File, |Download Count :------|:---------|:-------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Linux |32-bit |rush_linux_386.tar.gz | Linux |64-bit|rush_linux_amd64.tar.gz | Linux |arm64 |rush_linux_arm64.tar.gz | OS X |64-bit|rush_darwin_amd64.tar.gz | OS X |arm64 |rush_darwin_arm64.tar.gz | Windows|32-bit |rush_windows_386.exe.tar.gz | Windows|64-bit|rush_windows_amd64.exe.tar.gz | Windows|arm64 |rush_windows_arm64.exe.tar.gz | OpenBSD|64-bit|rush_openbsd_amd64.tar.gz | OpenBSD|arm64 |rush_openbsd_arm64.tar.gz | FreeBSD|64-bit|rush_freebsd_amd64.tar.gz | FreeBSD|arm64 |rush_freebsd_arm64.tar.gz |

Just download compressed executable file of your operating system, and decompress it with tar -zxvf *.tar.gz command or other tools. And then:

1. For Linux-like systems

sudo cp rush /usr/local/bin/

1. Or copy to anywhere in the environment variable PATH:

mkdir -p $HOME/bin/; cp rush $HOME/bin/

1. For windows, just copy rush.exe to C:\WINDOWS\system32.

Method 2: For Go developer

go install github.com/shenwei356/rush@latest

Method 3: Compiling from source

# download Go from https://go.dev/dl wget https://go.dev/dl/go1.25.5.linux-amd64.tar.gz tar -zxf go1.25.5.linux-amd64.tar.gz -C $HOME/ # or # echo "export PATH=$PATH:$HOME/go/bin" >> ~/.bashrc # source ~/.bashrc export PATH=$PATH:$HOME/go/bin git clone https://github.com/shenwei356/rush cd rush go build # or statically-linked binary CGO_ENABLED=0 go build -tags netgo -ldflags '-w -s' # or cross compile for other operating systems and architectures CGO_ENABLED=0 GOOS=openbsd GOARCH=amd64 go build -tags netgo -ldflags '-w -s'

Usage

rush -- a cross-platform command-line tool for executing jobs in parallel
Version: 0.10.0
Author: Wei Shen <[email protected]>
Homepage: https://github.com/shenwei356/rush
Input:
  - Input could be a list of strings or numbers, e.g., file paths.
  - Input can be given either from the STDIN or file(s) via the option -i/--infile.
  - Some options could be used to defined how the input records are parsed:
    -d, --field-delimiter   field delimiter in records (default "\s+")
    -D, --record-delimiter  record delimiter (default "\n")
    -n, --nrecords          number of records sent to a command (default 1)
    -J, --records-join-sep  record separator for joining multi-records (default "\n")
    -T, --trim              trim white space (" \t\r\n") in input
Output:
  - Outputs of all commands are written to STDOUT by default,
    you can also use -o/--out-file to specify a output file.
  - Outputs of all commands are random, you can use the flag -k/--keep-order
    to keep output in order of input.
  - Outputs of all commands are buffered, you can use the flag -I/--immediate-output
    to print output immediately and interleaved.
Replacement strings in commands:
  {}          full data
  {n}         nth field in delimiter-delimited data
  {/}         dirname
  {%}         basename
  {.}         remove the last file extension
  {:}         remove all file extensions.
  {^suffix}   remove suffix
  {@regexp}   capture submatch using regular expression.
              Limitation: curly brackets can't be used in the regexp.
  {#}         job ID
  {?}         a value computed as $cpus / $jobs, which can be used as the number of
              threads for each command. This value is dynamically adjusted according
              to the number of jobs (-j/--jobs).
Escaping curly brackets "{}":
    {{}}        {}
    {{1}}       {1}
    {{1,}}      {1,}
    {{a}}       {a}
Combinations:
    {%.}, {%:}            basename without extension
    {2.}, {2/}, {2%.}     manipulate nth field
    {file:}, {file:^_1}   remove all extensions of a preset variable (see below)
Preset variable (macro):
  1. You can pass variables to the command like awk via the option -v. E.g.,
     $ seq 3 | rush -v p=prefix_ -v s=_suffix 'echo {p}{}{s}'
     prefix_3_suffix
     prefix_1_suffix
     prefix_2_suffix
  2. A variable name should start with a letter and be followed by letters, digits, or underscores.
     A regular expression is used to check them: ^[a-zA-Z][A-Za-z0-9_]*$
  3. The value could also contain replacement strings.
     # {p} will be replaced with {%:}, which computes the basename and remove all file extensions.
     $ echo a/b/c.txt.gz | rush -v 'p={%:}' 'echo {p} {p}.csv'
     c c.csv
Usage:
  rush [flags] [command]
Examples:
  1. simple run, quoting is not necessary
      $ seq 1 10 | rush echo {}
  2. keep order
      $ seq 1 10 | rush 'echo {}' -k
  3. timeout
      $ seq 1 | rush 'sleep 2; echo {}' -t 1
  4. retry
      $ seq 1 | rush 'python script.py' -r 3
  5. dirname & basename & remove suffix
      $ echo dir/file_1.txt.gz | rush 'echo {/} {%} {^_1.txt.gz}'
      dir file.txt.gz dir/file
  6. basename without the last or any extension
      $ echo dir.d/file.txt.gz | rush 'echo {.} {:} {%.} {%:}'
      dir.d/file.txt dir.d/file file.txt file
  7. job ID, combine fields and other replacement strings
      $ echo 12 file.txt dir/s_1.fq.gz | rush 'echo job {#}: {2} {2.} {3%:^_1}'
      job 1: file.txt file s
  8. capture submatch using regular expression
      $ echo read_1.fq.gz | rush 'echo {@(.+)_\d}'
      read
  9. custom field delimiter
      $ echo a=b=c | rush 'echo {1} {2} {3}' -d =
      a b c
  10. custom record delimiter
      $ echo a=b=c | rush -D "=" -k 'echo {}'
      a
      b
      c
      $ echo abc | rush -D "" -k 'echo {}'
      a
      b
      c
  11. assign value to variable, like "awk -v"
      # seq 1 | rush 'echo Hello, {fname} {lname}!' -v fname=Wei,lname=Shen
      $ seq 1 | rush 'echo Hello, {fname} {lname}!' -v fname=Wei -v lname=Shen
      Hello, Wei Shen!
# preset variables support extra operations as well.
      echo read_1.fq.gz | ./rush -v 'p={:^_1}' -v 'f=a.s-10.txt' 'echo {} {p} {f:} {f@s\-(\d+)}'
      read_1.fq.gz read a 10
  12. preset variable (Macro)
      # equal to: echo sample_1.fq.gz | rush 'echo {:^_1} {} {:^_1}_2.fq.gz'
      $ echo sample_1.fq.gz | rush -v p={:^_1} 'echo {p} {} {p}_2.fq.gz'
      sample sample_1.fq.gz sample_2.fq.gz
  13. save successful commands to continue in NEXT run
      $ seq 1 3 | rush 'sleep {}; echo {}' -c -t 2
      [INFO] ignore cmd #1: sleep 1; echo 1
      [ERRO] run cmd #1: sleep 2; echo 2: time out
      [ERRO] run cmd #2: sleep 3; echo 3: time out
  14. escape special symbols
      $ seq 1 | rush 'echo -e "a\tb" | awk "{print $1}"' -q
      a
  15. escape curly brackets "{}"
      $ echo aaa bbb ccc | sed -E "s/(\S){3,}/\1/g"
      a b c
      $ echo 1 | rush 'echo aaa bbb ccc | sed -E "s/(\S){{3,}}/\1/g"' --dry-run
      echo aaa bbb ccc | sed -E "s/(\S){3,}/\1/g"
  16. run a command with relative paths in Windows, please use backslash as the separator.
      # "brename -l -R" is used to search paths recursively
      $ brename -l -q -R -i -p "\.go$" | rush "bin\app.exe {}"
More examples: https://github.com/shenwei356/rush
Flags:
  -v, --assign strings            assign the value val to the variable var (format: var=val, val also
                                  supports replacement strings)
      --cleanup-time int          time to allow child processes to clean up between stop / kill signals
                                  (unit: seconds, 0 for no time) (default 3) (default 3)
  -c, --continue                  continue jobs. NOTES: 1) successful commands are saved in file (given
                                  by flag -C/--succ-cmd-file); 2) if the file does not exist, rush saves
                                  data so we can continue jobs next time; 3) if the file exists, rush
                                  ignores jobs in it and update the file
      --dry-run                   print command but not run
  -q, --escape                    escape special symbols like $ which you can customize by flag
                                  -Q/--escape-symbols
  -Q, --escape-symbols string     symbols to escape (default "$#&")
      --eta                       show ETA progress bar
  -d, --field-delimiter string    field delimiter in records, support regular expression (default "\\s+")
  -h, --help                      help for rush
  -I, --immediate-output          print output immediately and interleaved, to aid debugging
  -i, --infile strings            input data file, multi-values supported
  -j, --jobs int                  run n jobs in parallel (default value depends on your device) (default 16)
  -k, --keep-order                keep output in order of input
      --no-kill-exes strings      exe names to exclude from kill signal, example: mspdbsrv.exe; or use
                                  all for all exes (default none)
      --no-stop-exes strings      exe names to exclude from stop signal, example: mspdbsrv.exe; or use
                                  all for all exes (default none)
  -n, --nrecords int              number of records sent to a command (default 1)
  -o, --out-file string           out file ("-" for stdout) (default "-")
      --print-retry-output        print output from retry commands (default true)
      --propagate-exit-status     propagate child exit status up to the exit status of rush (default true)
  -D, --record-delimiter string   record delimiter (default is "\n") (default "\n")
  -J, --records-join-sep string   record separator for joining multi-records (default is "\n") (default "\n")
  -r, --retries int               maximum retries (default 0)
      --retry-interval float      retry interval (unit: second, supports fractions like 0.5) (default 0)
  -e, --stop-on-error             stop child processes on first error (not perfect, you may stop it by
                                  typing ctrl-c or closing terminal)
  -C, --succ-cmd-file string      file for saving successful commands (default "successful_cmds.rush")
  -t, --timeout int               timeout of a command (unit: seconds, 0 for no timeout) (default 0)
  -T, --trim string               trim white space (" \t\r\n") in input (available values: "l" for left,
                                  "r" for right, "lr", "rl", "b" for both side)
      --verbose                   print verbose information
  -V, --version                   print version information and check for update

1. Read data from file (-i)

1. Keep output order (-k)

1. Timeout (-t)

1. Retry (-r)

1. Input containing {} (since v0.10.0)

1. Output {} itself (since v0.7.0)

1. Dirname ({/}) and basename ({%}) and remove custom suffix ({^suffix})

1. Get basename, and remove last ({.}) or any ({:}) extension

1. Capture submatch using regular expression ({@regexp})

1. Custom field delimiter (-d)

1. Send multi-lines to every command (-n)

# Multiple records are joined with separator "\n" (-J/--records-join-sep) $ seq 5 | rush -n 2 -k 'echo "{}"; echo' -J ' ' 1 2

1. Custom record delimiter (-D), note that empty records are not used.

1. Assign value to variable, like awk -v (-v)

1. Preset variable (-v), avoid repeatedly writing verbose replacement strings

1. Interrupt jobs by Ctrl-C, rush will stop unfinished commands and exit.

- Linux: rush sends SIGINT to every marked child process, waits up to --cleanup-time, and then sends SIGKILL to any remaining processes using native system calls. - Windows: rush starts each command in a new process group and sends that group a directed Ctrl+Break, followed by forced tree cleanup. Windows cannot direct Ctrl+C to a child group; a user Ctrl+C still makes rush exit with status 130. - Unix Ctrl+C exits with status 130 and SIGTERM exits with status 143. A command timeout exits with status 124. - Cleanup covers ordinary descendants that remain in the Unix process group or Windows parent/child tree. Processes that deliberately detach, daemonize, create a new console/session, or use Windows breakaway are outside this guarantee.

Press Ctrl-C again to skip the remaining cleanup delay and immediately kill unfinished processes. Commands that have not started are discarded after the interrupt and are not executed.

1. Continue/resume jobs (-c). When some jobs failed (by execution failure, timeout,

Commands are saved to file (-C) right after it finished, so we can view the check finished jobs:

1. A bioinformatics example: mapping with bwa, and processing result with samtools:

Since {}/{%} appears many times, we can use preset variable (macro) to simplify it:

• Shell grep returns exit code 1 when no matches found.

Specially thank @brentp and his gargs, from which rush` borrows some ideas.

Thank @bburgin for his contribution on improvement of child process management.

Contact

Create an issue to report bugs, propose new functions or ask for help.

License

MIT License