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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 18).

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, e.g. the first half of a line is from one process and the last half of the line is from another process. (--line-buffer in GNU parallel)
Timeout (-t). (--timeout in GNU parallel)
Retry (-r). (--retry-failed --joblog in GNU parallel)
Safe exit after capturing Ctrl-C (not perfect, you may stop it by typing ctrl-c or closing terminal)
Continue (-c). (--resume --joblog in GNU parallel, <s/>sut it does not support multi-line commands, which are common in workflow</s>)
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(s) (-e). (not perfect, you may stop it by typing ctrl-c or closing terminal) (--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):
- {{}}, "{}" itself
- {#}, job ID. (Same in GNU parallel)
- {}, full data. (Same in GNU parallel)
- {n}, nth field in delimiter-delimited data. (Same in GNU parallel)
- Directory and file
  - {/}, dirname. ({//} in GNU parallel)
  - {%}, basename. ({/} in GNU parallel)
  - {.}, remove the last file extension. (Same in GNU parallel)
  - {:}, remove all file extensions (Not directly supported in GNU parallel)
  - {^suffix}, remove suffix (Not directly supported in GNU parallel)
  - {@regexp}, capture submatch using regular expression (Not directly supported in GNU parallel)
- Combinations
  - {%.}, {%:}, basename without extension
  - {2.}, {2/}, {2%.}, manipulate nth field
Preset variable (macro), e.g., rush -v p={^suffix} 'echo {p}_new_suffix', where {p} is replaced with {^suffix}. (Using Shell variable in GNU parallel)

Minor:

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

Differences between rush and GNU parallel on GNU parallel site.

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 v0.6.0

Tip: run rush -V to check update !!!

OS	Arch	File, (中国镜像)
Linux	32-bit	rush_linux_386.tar.gz, (mirror)
Linux	64-bit	rush_linux_amd64.tar.gz, (mirror)
Linux	arm64	rush_linux_arm64.tar.gz, (mirror)
OS X	64-bit	rush_darwin_amd64.tar.gz, (mirror)
OS X	arm64	rush_darwin_arm64.tar.gz, (mirror)
Windows	32-bit	rush_windows_386.exe.tar.gz, (mirror)
Windows	64-bit	rush_windows_amd64.exe.tar.gz, (mirror)

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

For Linux-like systems
1. If you have root privilege simply copy it to /usr/local/bin:
```
 sudo cp rush /usr/local/bin/
```
2. Or copy to anywhere in the environment variable PATH:
```
 mkdir -p $HOME/bin/; cp rush $HOME/bin/
```
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/go1.17.13.linux-amd64.tar.gz

tar -zxf go1.17.13.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: 0.5.7

Author: Wei Shen <shenwei356@gmail.com>

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/--kep-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
  {#}         job ID
  {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
  {{}}        "{}" itself

  Combinations:
    {%.}, {%:}          basename without extension
    {2.}, {2/}, {2%.}   manipulate nth field

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. 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!
  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. 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 int        retry interval (unit: second) (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

Examples

Simple run, quoting is not necessary

 # seq 1 3 | rush 'echo {}'
 $ seq 1 3 | rush echo {}
 3
 1
 2

Read data from file (-i)

 $ rush echo {} -i data1.txt -i data2.txt

Keep output order (-k)

 $ seq 1 3 | rush 'echo {}' -k
 1
 2
 3

Timeout (-t)

 $ time seq 1 | rush 'sleep 2; echo {}' -t 1
 [ERRO] run command #1: sleep 2; echo 1: time out

 real    0m1.010s
 user    0m0.005s
 sys     0m0.007s

Retry (-r)

 $ seq 1 | rush 'python unexisted_script.py' -r 1
 python: can't open file 'unexisted_script.py': [Errno 2] No such file or directory
 [WARN] wait command: python unexisted_script.py: exit status 2
 python: can't open file 'unexisted_script.py': [Errno 2] No such file or directory
 [ERRO] wait command: python unexisted_script.py: exit status 2

Input containing {} (since v0.6.0)

 $ echo "a attr{href}"="h4 text{}" | rush -T b -k -D "=" 'echo "{}"'
 a attr{href}
 h4 text{}

 $ echo -ne "a{},b{{}},c{d}" | rush -D , -k "echo {}"
 a{}
 b{{}}
 c{d}

Output {} itself (since v0.6.0)

 $ echo abc | rush 'echo "{} {{}}"'
 abc {}

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

 $ echo dir/file_1.txt.gz | rush 'echo {/} {%} {^_1.txt.gz}'
 dir file_1.txt.gz dir/file

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

 $ echo dir.d/file.txt.gz | rush 'echo {.} {:} {%.} {%:}'
 dir.d/file.txt dir.d/file file.txt file

Job ID, combine fields index 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

Capture submatch using regular expression ({@regexp})
```
 $ echo read_1.fq.gz | rush 'echo {@(.+)_\d}'
```

Custom field delimiter (-d)

 $ echo a=b=c | rush 'echo {1} {2} {3}' -d =
 a b c

Send multi-lines to every command (-n)

 $ seq 5 | rush -n 2 -k 'echo "{}"; echo'
 1
 2

 3
 4

 5

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

 3 4

 5

 $ seq 5 | rush -n 2 -k -j 3 'echo {1}'
 1
 3
 5

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

 $ echo a b c d | rush -D " " -k 'echo {}'
 a
 b
 c
 d

 $ echo abcd | rush -D "" -k 'echo {}'
 a
 b
 c
 d

 # FASTA format
 $ echo -ne ">seq1\nactg\n>seq2\nAAAA\n>seq3\nCCCC"
 >seq1
 actg
 >seq2
 AAAA
 >seq3
 CCCC

 $ echo -ne ">seq1\nactg\n>seq2\nAAAA\n>seq3\nCCCC" | rush -D ">" 'echo FASTA record {#}: name: {1} sequence: {2}' -k -d "\n"
 FASTA record 1: name: seq1 sequence: actg
 FASTA record 2: name: seq2 sequence: AAAA
 FASTA record 3: name: seq3 sequence: CCCC

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

 $ seq 1  | rush 'echo Hello, {fname} {lname}!' -v fname=Wei -v lname=Shen
 Hello, Wei Shen!

 $ seq 1  | rush 'echo Hello, {fname} {lname}!' -v fname=Wei,lname=Shen
 Hello, Wei Shen!

 $ for var in a b; do \
 $   seq 1 3 | rush -k -v var=$var 'echo var: {var}, data: {}'; \
 $ done
 var: a, data: 1
 var: a, data: 2
 var: a, data: 3
 var: b, data: 1
 var: b, data: 2
 var: b, data: 3

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

 # naive way
 $ echo read_1.fq.gz | rush 'echo {:^_1} {:^_1}_2.fq.gz'
 read read_2.fq.gz

 # macro + removing suffix
 $ echo read_1.fq.gz | rush -v p='{:^_1}' 'echo {p} {p}_2.fq.gz'

 # macro + regular expression
 $ echo read_1.fq.gz | rush -v p='{@(.+?)_\d}' 'echo {p} {p}_2.fq.gz'

Escape special symbols

 $ seq 1 | rush 'echo "I have $100"'
 I have 00
 $ seq 1 | rush 'echo "I have $100"' -q
 I have $100
 $ seq 1 | rush 'echo "I have $100"' -q --dry-run
 echo "I have \$100"

 $ seq 1 | rush 'echo -e "a\tb" | awk "{print $1}"'
 a       b

 $ seq 1 | rush 'echo -e "a\tb" | awk "{print $1}"' -q
 a

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

 $ seq 1 20 | rush 'sleep 1; echo {}'
 ^C[CRIT] received an interrupt, stopping unfinished commands...
 [ERRO] wait cmd #7: sleep 1; echo 7: signal: interrupt
 [ERRO] wait cmd #5: sleep 1; echo 5: signal: killed
 [ERRO] wait cmd #6: sleep 1; echo 6: signal: killed
 [ERRO] wait cmd #8: sleep 1; echo 8: signal: killed
 [ERRO] wait cmd #9: sleep 1; echo 9: signal: killed
 1
 3
 4
 2

Continue/resume jobs (-c). When some jobs failed (by execution failure, timeout, or cancelling by user with Ctrl + C), please switch flag -c/--continue on and run again, so that rush can save successful commands and ignore them in NEXT run.

 $ seq 1 3 | rush 'sleep {}; echo {}' -t 3 -c
 1
 2
 [ERRO] run cmd #3: sleep 3; echo 3: time out

 # successful commands:
 $ cat successful_cmds.rush
 sleep 1; echo 1__CMD__
 sleep 2; echo 2__CMD__

 # run again
 $ seq 1 3 | rush 'sleep {}; echo {}' -t 3 -c
 [INFO] ignore cmd #1: sleep 1; echo 1
 [INFO] ignore cmd #2: sleep 2; echo 2
 [ERRO] run cmd #1: sleep 3; echo 3: time out

Commands of multi-lines (Not supported in GNU parallel)

 $ seq 1 3 | rush 'sleep {}; echo {}; \
 echo finish {}' -t 3 -c -C finished.rush
 1
 finish 1
 2
 finish 2
 [ERRO] run cmd #3: sleep 3; echo 3; \
 echo finish 3: time out

 $ cat finished.rush
 sleep 1; echo 1; \
 echo finish 1__CMD__
 sleep 2; echo 2; \
 echo finish 2__CMD__

 # run again
 $ seq 1 3 | rush 'sleep {}; echo {}; \
 echo finish {}' -t 3 -c -C finished.rush
 [INFO] ignore cmd #1: sleep 1; echo 1; \
 echo finish 1
 [INFO] ignore cmd #2: sleep 2; echo 2; \
 echo finish 2
 [ERRO] run cmd #1: sleep 3; echo 3; \
 echo finish 3: time out

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

 grep -c __CMD__ successful_cmds.rush

A comprehensive example: downloading 1K+ pages given by three URL list files using phantomjs save_page.js (some page contents are dynamicly generated by Javascript, so wget does not work). Here I set max jobs number (-j) as 20, each job has a max running time (-t) of 60 seconds and 3 retry changes (-r). Continue flag -c is also switched on, so we can continue unfinished jobs. Luckily, it's accomplished in one run :smile:
```
 $ for f in $(seq 2014 2016); do \
 $    /bin/rm -rf $f; mkdir -p $f; \
 $    cat $f.html.txt | rush -v d=$f -d = 'phantomjs save_page.js "{}" > {d}/{3}.html' -j 20 -t 60 -r 3 -c; \
 $ done
```

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

 $ tree raw.cluster.clean.mapping
 raw.cluster.clean.mapping
 ├── M1
 │   ├── M1_1.fq.gz -> ../../raw.cluster.clean/M1/M1_1.fq.gz
 │   ├── M1_2.fq.gz -> ../../raw.cluster.clean/M1/M1_2.fq.gz
 ...

 $ ref=ref/xxx.fa
 $ threads=25
 $ ls -d raw.cluster.clean.mapping/* \
     | rush -v ref=$ref -v j=$threads \
         'bwa mem -t {j} -M -a {ref} {}/{%}_1.fq.gz {}/{%}_2.fq.gz > {}/{%}.sam; \
         samtools view -bS {}/{%}.sam > {}/{%}.bam; \
         samtools sort -T {}/{%}.tmp -@ {j} {}/{%}.bam -o {}/{%}.sorted.bam; \
         samtools index {}/{%}.sorted.bam; \
         samtools flagstat {}/{%}.sorted.bam > {}/{%}.sorted.bam.flagstat; \
         /bin/rm {}/{%}.bam {}/{%}.sam;' \
         -j 2 --verbose -c -C mapping.rush

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

 $ ls -d raw.cluster.clean.mapping/* \
     | rush -v ref=$ref -v j=$threads -v p='{}/{%}' \
         'bwa mem -t {j} -M -a {ref} {p}_1.fq.gz {p}_2.fq.gz > {p}.sam; \
         samtools view -bS {p}.sam > {p}.bam; \
         samtools sort -T {p}.tmp -@ {j} {p}.bam -o {p}.sorted.bam; \
         samtools index {p}.sorted.bam; \
         samtools flagstat {p}.sorted.bam > {p}.sorted.bam.flagstat; \
         /bin/rm {p}.bam {p}.sam;' \
         -j 2 --verbose -c -C mapping.rush

Special Cases

Shell grep returns exit code 1 when no matches found. rush thinks it failed to run. Please use grep foo bar || true instead of grep foo bar.

  $ seq 1 | rush 'echo abc | grep 123'
  [ERRO] wait cmd #1: echo abc | grep 123: exit status 1
  $ seq 1 | rush 'echo abc | grep 123 || true'

Contributors

Main contributors:

Wei Shen
@bburgin Brian Burgin for cross-platform process management.
@howeyc Chris Howey for ETA progress bar.

Others contributors

Acknowledgements

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

Starchart