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SciWIn Client

SciWIn-Client

SciWI-Client helps scientists build, run, and publish complex computational workflows — making research more reproducible, scalable, and collaborative.
Installation Documentation 
$ s4n --help
$ s4n tool create python calculation.py --population population.csv --speakers speakers.csv
$ s4n run python plot.py --results results.csv
$ s4n workflow create main
$ s4n workflow connect main --from @inputs/speakers --to calculation/speakers
$ s4n execute local workflows/main/main.cwl inputs.yml
Terminal Window 
 $ s4n --help
 _____        _  _    _  _____         _____  _  _               _   
/  ___|      (_)| |  | ||_   _|       /  __ \| |(_)             | |   
\ `--.   ___  _ | |  | |  | |  _ __   | /  \/| | _   ___  _ __  | |_  
 `--. \ / __|| || |/\| |  | | | '_ \  | |    | || | / _ \| '_ \ | __|
/\__/ /| (__ | |\  /\  / _| |_| | | | | \__/\| || ||  __/| | | || |_  
\____/  \___||_| \/  \/  \___/|_| |_|  \____/|_||_| \___||_| |_| \__|
Client tool for Scientific Workflow Infrastructure (SciWIn)
Documentation: https://fairagro.github.io/m4.4_sciwin_client/
Version: 0.6.1
Usage: s4n <COMMAND>
Commands:
   init         Initializes project folder structure and repository
   tool         Provides commands to create and work with CWL CommandLineTools
   workflow     Provides commands to create and work with CWL Workflows
   annotate     Annotate CWL files
   execute      Execution of CWL Files locally or on remote servers [aliases: ex]
   sync         
   completions  Generate shell completions
   help         Print this message or the help of the given subcommand(s)
Options:
   -h, --help     Print help
   -V, --version  Print version
 $ s4n tool create python calculation.py --population population.csv --speakers speakers.csv
📂 The current working directory is /home/ubuntu/sciwin_test
▶️  Executing command: python calculation.py --population population.csv --speakers speakers.csv
Total population: 7694245029
            language    speakers  percentage
0             Bangla   300000000    3.899018
1    Egyptian Arabic   100542400    1.306722
2            English  1132366680   14.717060
3             German   134993040    1.754468
4         Indonesian   198996550    2.586304
5           Japanese   128000000    1.663581
6         Portuguese   475300000    6.177344
7            Punjabi   125000000    1.624591
8            Russian   154000000    2.001496
9  Standard Mandarin  1090951810   14.178803
📜 Found changes:
        - results.csv
📄 Created CWL file workflows/calculation/calculation.cwl
 $ s4n run python plot.py --results results.csv
📂 The current working directory is /home/ubuntu/sciwin_test
▶️  Executing command: python plot.py --results results.csv
📜 Found changes:
        - results.svg
📄 Created CWL file workflows/plot/plot.cwl
 $ s4n workflow create main
📄 Created new Workflow file: workflows/main/main.cwl
        1 | + #!/usr/bin/env cwl-runner
        2 | + 
        3 | + cwlVersion: v1.2
        4 | + class: Workflow
        5 | + 
        6 | + inputs: []
        7 | + outputs: []
        8 | + steps: []
 $ s4n workflow connect main --from @inputs/speakers --to calculation/speakers
➕ Added step calculation to workflow
➕ Added or updated connection from inputs.speakers to calculation/speakers in workflow
✔️  Updated Workflow workflows/main/main.cwl!
   3    3 |   cwlVersion: v1.2
   4    4 |   class: Workflow
   5    5 |   
   6      | - inputs: []
        6 | + inputs:
        7 | + - id: speakers
        8 | +   type: File
        9 | + 
   7   10 |   outputs: []
   8      | - steps: []
       11 | + steps:
       12 | + - id: calculation
       13 | +   in:
       14 | +   - id: speakers
       15 | +     source: speakers
       16 | +   run: ../calculation/calculation.cwl
       17 | +   out:
       18 | +   - results
 $ s4n execute local workflows/main/main.cwl inputs.yml
🚲 Executing Tool "workflows/main/../calculation/calculation.cwl" ...
📁 Created staging directory: "/tmp/.tmpAz2l9s"
⏳ Executing Command: `python workflows/calculation/calculation.py --population /tmp/.tmpAz2l9s/data/population.csv --speakers /tmp/.tmpAz2l9s/data/speakers_revised.csv`
Total population: 7694245029
            language    speakers  percentage
0             Bangla   300000000    3.899018
1    Egyptian Arabic   100542400    1.306722
2            English  1132366680   14.717060
3             German   134993040    1.754468
4         Indonesian   198996550    2.586304
5           Japanese   128000000    1.663581
6         Portuguese   475300000    6.177344
7            Punjabi   125000000    1.624591
8            Russian   154000000    2.001496
9  Standard Mandarin  1090951810   14.178803
📜 Wrote output file: "/tmp/.tmpmzpkus/results.csv"
✔️  Tool "workflows/main/../calculation/calculation.cwl" executed successfully in 623ms!
🚲 Executing Tool "workflows/main/../plot/plot.cwl" ...
📁 Created staging directory: "/tmp/.tmprbR7MR"
⏳ Executing Command: `python workflows/plot/plot.py --results /tmp/.tmprbR7MR/.tmpmzpkus/results.csv`
📜 Wrote output file: "/tmp/.tmpmzpkus/results.svg"
✔️  Tool "workflows/main/../plot/plot.cwl" executed successfully in 2s!
✔️  Workflow "workflows/main/main.cwl" executed successfully in 2s!
{
  "out": {
    "class": "File",
    "location": "file:///mnt/hello_world/results.svg",
    "path": "/mnt/hello_world/results.svg",
    "basename": "results.svg",
    "nameroot": "results",
    "nameext": ".svg",
    "checksum": "sha1$8e59fcb5729b9576c7f721ef9f63057b09e738f8",
    "size": 75260
  }
}

Examples

Section titled “Examples”

Get started

Section titled “Get started”

  1. Install SciWIn-Client

    Section titled “Install SciWIn-Client”
    The easiest way to install s4n is to use the installer scripts.

    Linux

    Terminal window
    curl --proto '=https' --tlsv1.2 -LsSf https://fairagro.github.io/m4.4_sciwin_client/get_s4n.sh | sh

    Windows

    Terminal window
    powershell -ExecutionPolicy Bypass -c "irm https://fairagro.github.io/m4.4_sciwin_client/get_s4n.ps1 | iex"

  2. Initialize Project

    Section titled “Initialize Project”
    Initialize a SciWIn Project in your code repository
    Terminal window
    s4n init

  3. Start creating Workflows

    Section titled “Start creating Workflows”
    Using the s4n tool and s4n workflow commands you can built your reusable data pipelines stepwise.
    Terminal window
    s4n tool create echo "Hello World"