semvec/pypi-packages huggingface dataset:
dbp 18.12.3
Simple program to manage gbp-docker container lifecycle.
Requires Python: >=3.5,<4

# Docker-buildpackage

[![PyPI version](https://badge.fury.io/py/dbp.svg)](https://pypi.org/project/dbp/)
[![CalVer](https://img.shields.io/badge/calver-YY.0M.MICRO-blue.svg)](https://pypi.org/project/dbp/)
[![Build status](https://badge.buildkite.com/1767c846c36bcae205347eb72a5396be1474608249b0849f16.svg)](https://buildkite.com/opx/opx-infra-dbp)
[![codecov](https://codecov.io/gh/opx-infra/dbp/branch/master/graph/badge.svg)](https://codecov.io/gh/opx-infra/dbp)

Docker-buildpackage is a tool for building OpenSwitch Debian packages.

## Summary

* Docker-buildpackage has two parts: a cli app (`dbp`) and a Docker image ([`opxhub/gbp`](https://github.com/opx-infra/gbp-docker))
* `dbp` manages the Docker image and container lifecycle
* `dbp` resolves the local build dependency graph
* `dbp` runs [Git-buildpackage](https://honk.sigxcpu.org/piki/projects/git-buildpackage/) with [this configuration](https://github.com/opx-infra/gbp-docker/blob/master/assets/gbp.conf) to build packages
* Git-buildpackage runs [Debuild](https://manpages.debian.org/stretch/devscripts/debuild.1.en.html) with [this configuration](https://github.com/opx-infra/gbp-docker/blob/master/assets/devscripts) to build packages

## Install

```bash
pip3 install dbp
```

## Docs

Get started with the [documentation](https://opx-infra.github.io/dbp/).

## Support

For bug reports and feature requests, file an issue on [GitHub](https://github.com/opx-infra/dbp/issues/new/choose). For other support, drop by the [*dbp* support channel](https://chat.openswitch.net/channel/dbp) and we'll help you out.
cwl-airflow-parser 1.0.20181213213631
Package extends Airflow functionality with CWL v1.0 support

# cwl-airflow-parser

### About
Extends **[Apache-Airflow](https://github.com/apache/incubator-airflow)** with **[CWL v1.0](http://www.commonwl.org/v1.0/)** support.

### Installation

```sh
pip3.6 install -U cwl-airflow-parser
```

### Requirements
Package has been tested on Ubuntu 16.04.3 and Mac OS X Sierra/ High Sierra. Make sure your system satisfies the following criteria:
- python 3.6
- [docker](https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/)
- nodejs

### Usage

```python
from cwl_airflow_parser import CWLDAG, CWLJobDispatcher, CWLJobGatherer
from datetime import timedelta

def cwl_workflow(workflow_file):
    dag = CWLDAG(default_args={
        'owner': 'airflow',
        'email': ['my@email.com'],
        'email_on_failure': False,
        'email_on_retry': False,
        'retries': 20,
        'retry_exponential_backoff': True,
        'retry_delay': timedelta(minutes=30),
        'max_retry_delay': timedelta(minutes=60 * 4)
    },
        cwl_workflow=workflow_file)
    dag.create()
    dag.add(CWLJobDispatcher(dag=dag), to='top')
    dag.add(CWLJobGatherer(dag=dag), to='bottom')

    return dag
 
cwl_workflow("/path/to/my/workflow.cwl")
```
biowardrobe-cwl-workflows 1.0.20181213214400
Wrapped BioWardrobe's CWL files

[![Build Status](https://travis-ci.org/datirium/workflows.svg?branch=master)](https://travis-ci.org/datirium/workflows)
# Workflows
CWL workflows for [BioWardrobe](https://biowardrobe.com/) project. This package includes 
 all the original BioWardrobe's pipelines, simplifies import 
for biowardrobe-airflow-analysis. It also includes extra pipelines for new project SciDAP.

## Install 

```sh
pip3 install biowardrobe-cwl-workflows
```
or from sources
```sh
git clone https://github.com/datirium/workflows
pip3 install .
```

## Usage

```python
from biowardrobe_cwl_workflows import available
_path_to_workflow=available(workflow='chipseq-se.cwl')
```

## Extra features in CWL

### Metadata & Upstreams
```yaml
'sd:metadata':
  - "../metadata/chipseq-header.cwl"

'sd:upstream':
  genome_indices: "genome-indices.cwl"
  control_file: "chipseq-se.cwl"

```

To enable users to extend user interface (dynamic form) with extra input fields not required by a workflow ```'sd:metadata'``` field were introduced. It defines a list of workflows where inputs field just used for constructing and storing the input object. 


To simplify selection of already analyzed common data ```’sd:upstream’``` were introduced. It defines the upstream workflows of the process. The process is ready to run when upstream output data is available. 


##### Example of extra input fields for user interface:

```yaml
cwlVersion: v1.0
class: Workflow

inputs:
  cells:
    type: string
    label: "Cells"
    sd:preview:
      position: 1
  conditions:
    type: string
    label: "Conditions"
    sd:preview:
      position: 3
  alias:
    type: string
    label: "Experiment short name/Alias"
    sd:preview:
      position: 2
  catalog:
    type: string?
    label: "Catalog #"
  description:
    type: string?
    'sd:type': 'text'
    label: "Description"

outputs: []
steps: []

```

### CWL VisualPlugins for output data

```yaml
outputs:
  ...
  fastx_statistics:
    type: File
    label: "FASTQ statistics"
    format: "http://edamontology.org/format_2330"
    doc: "fastx_quality_stats generated FASTQ file quality statistics file"
    outputSource: fastx_quality_stats/statistics_file
    'sd:visualPlugins':
    - line:
      Title: 'Base frequency plot'
      xAxisTitle: 'Nucleotide position'
      yAxisTitle: 'Frequency'
      colors: ["#b3de69", "#99c0db", "#fb8072", "#fdc381", "#888888"]
      data: [$12, $13, $14, $15, $16]
  ...
```