Metadata-Version: 2.1
Name: pybrave
Version: 0.1.9
Summary: Bioinformatics Reactive Analysis and Visualization Engine
Author: WangYang
Project-URL: Source, https://github.com/pybrave/brave
Project-URL: Tracker, https://github.com/pybrave/brave
Project-URL: Documentation, https://github.com/pybrave/brave
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: fastapi
Requires-Dist: sqlalchemy
Requires-Dist: pandas
Requires-Dist: uvicorn[standard]
Requires-Dist: typer
Requires-Dist: pymysql
Requires-Dist: click ==8.1.8
Requires-Dist: dependency-injector <5.0,>=4.0
Requires-Dist: docker
Requires-Dist: kubernetes
Requires-Dist: psutil
Requires-Dist: httpx
Requires-Dist: nbformat

<p align="center">
  <img src="https://raw.githubusercontent.com/pybrave/brave/refs/heads/master/brave/frontend/img/logo.png" alt="brave" style="width: 500px;">
</p>
<p align="center" style="font-size: 1.5em;">
    <em>Bioinformatics Reactive Analysis and Visualization Engine</em>
</p>

<a href="https://pypi.org/project/pybrave" target="_blank">
    <img src="https://img.shields.io/pypi/v/pybrave?color=%2334D058&label=pypi%20package" alt="Package version">
</a>


## Installation
```
pip install pybrave
```

## Usage
```
brave
```
+ <http://localhost:5000>


install pipeline
```
git clone https://github.com/pybrave/pipeline-metagenomics.git ~/.brave/pipeline/7530139e-8985-423f-9fb6-32650828ca40

```

![](https://raw.githubusercontent.com/pybrave/brave/refs/heads/master/images/install.png)


```
brave --base-dir /ssd1/wy/workspace2/nextflow_workspace \
    --work-dir /data/wangyang/nf_work \
    --pipeline-dir /ssd1/wy/workspace2/nextflow-fastapi/pipeline-dev \
    --literature-dir /ssd1/wy/workspace2/nextflow-fastapi/literature \
    --db-type mysql --mysql-url root:123456@192.168.3.60:53306/pipeline  \
    --port 5000
```

## docker 
```
mkdir $PWD/data
docker run --rm -p 5000:5000  \
  --user $(id -u):$(id -g) \
  -v  /var/run/docker.sock:/var/run/docker.sock  \
  -v /tmp/brave.sock:/tmp/brave.sock \
  -v $PWD/data:/.brave \
  registry.cn-hangzhou.aliyuncs.com/wybioinfo/pybrave

git clone https://github.com/pybrave/pipeline-metagenomics.git  $PWD/data/pipeline/7530139e-8985-423f-9fb6-32650828ca40
```
```
docker run --rm -p 5000:5000  \
  --user $(id -u):$(id -g) \
 --group-add $(stat -c '%g' /var/run/docker.sock) \
  -v  /var/run/docker.sock:/var/run/docker.sock  \
  -v /tmp/brave.sock:/tmp/brave.sock \
  -v ~/.brave:/.brave \
  -v /ssd1:/ssd1 \
  -v /data:/data \
  registry.cn-hangzhou.aliyuncs.com/wybioinfo/pybrave \
  brave --pipeline-dir /ssd1/wy/workspace2/nextflow-fastapi/pipeline-dev \
  --base-dir /ssd1/wy/workspace2/nextflow_workspace \
  --work-dir /data/wangyang/nf_work \
  --literature-dir /ssd1/wy/workspace2/nextflow-fastapi/literature \
  --db-type mysql \
  --mysql-url root:123456@192.168.3.60:53306/pipeline \
  --port 5000 
```

                
## development
```
mkdir -p development/pipeline-dev
mkdir -p development/base-dev 
python  -m brave \
   --port 5000 \
   --pipeline-dir development/pipeline-dev \
   --base-dir development/base-dev 
git clone https://github.com/pybrave/pipeline-metagenomics.git  development/pipeline-dev/7530139e-8985-423f-9fb6-32650828ca40
```

## contact
+ 1749748955@qq.com
