Metadata-Version: 2.1
Name: dry-pipe
Version: 0.2.2
Summary: A Python DSL for bioinformatics pipelines
Home-page: https://github.com/calculs-ca/DryPipe
Author: Maxime Lévesque
Author-email: maxime.levesque@gmail.com
Project-URL: Bug Tracker, https://github.com/calculs-ca/DryPipe/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Requires-Dist: click (==8.1.3)
Requires-Dist: uvicorn (==0.17.6)
Requires-Dist: python-socketio (==5.6.0)
Requires-Dist: psutil (==5.9.1)
Requires-Dist: rich (==12.4.4)
Requires-Dist: requests (==2.27.1)
Requires-Dist: sshkeyboard (==2.3.1)
Provides-Extra: full
Requires-Dist: PyYAML (==5.4.1) ; extra == 'full'
Requires-Dist: paramiko (==2.11.0) ; extra == 'full'

# DryPipe

## A Python DSL for bioinformatics pipelines


## Getting Started

#### 1 Install dry-pipe in your virtualenv

```shell
    pyton3.8 -m venv your_venv 
    source your_venv/bin/activate
    pip install dry-pipe
```

#### 2 Write your  pipeline

```python

    from dry_pipe import DryPipe
    
    def my_pipeline_task_generator(dsl):
        yield dsl.task(key="task1") 
            .consumes(x=dsl.val(123)) 
            .produces(result=dsl.file("f.txt"))
            .calls("""
                #!/usr/bin/env bash                
                echo $x > $result
            """)
        
    def my_pipeline():
        return DryPipe.create_pipeline(my_pipeline_task_generator)
```

#### 3 Run it
(assuming the above code is in module my_module.py)
```shell
    drypipe run --pipeline='my_module:my_pipeline'
```
