# PopGenomics CLI on multi cloud platform
## 简介
Popgenomics CLI是由百奥云数据科技有限公司开发的面向农业育种客户的大规模群体基因组计算多云基础设施工具，能够帮助农业育种客户实现数千规模群体基因组的低成本，高效率，自动化的群体基因组计算作业。
## 安装
本软件需要`Python3.9`及以上版本，并需要安装相关Pyhton包的依赖。
若网络环境较好可以直接使用pip 安装
```
$ pip install popgen-biobin
```
若网络环境不好，可以根据情况使用合适的镜像源手动安装需要的Python包
requirements.txt 内容如下：
```
cement==3.0.8
cement[jinja2]
cement[yaml]
cement[colorlog]
polling2
alibabacloud_easygene20210315==1.1.1
requests
volcengine-python-sdk
volcengine
tabulate
tinydb
miniwdl
pandas
numpy
```
```
$ pip install -r requirements.txt
$ pip install popgen-biobin
```
## 使用说明
首先需要获取具有相关云计算平台权限的AK/SK
### 阿里云 基因分析平台
账号的AK/SK需要具有数据所在对象存储OSS的读写权限以及基因分析平台的使用权限。
#### 功能列表
1. config 配置平台AS/SK和endpiont
2. create-app 上传WDL工作流作为应用APP
3. create-run 提交单个工作流任务
4. create-submission 批量投递工作流任务
5. get-run 查询单个工作流任务状态
6. get-submission 查询批量投递工作流任务状态
7. list-apps 查询工作空间中的应用APP
8. list-runs 查询投递任务的运行详情
9. list-workspaces 查询拥有的工作空间
#### 使用步骤
1. 配置AK/SK以及endpoint，如北京的endpiont为：easygene.cn-beijing.aliyuncs.com
```
$ popgen ali config
Enter ACCESS KEY ID:
Enter ACCESS KEY SECRET:
Enter endpoint:
```
2. 验证使用权限
```
$ popgen ali list-workspaces
```
若正常列出具有的工作空间，则说明具有基因分析平台的使用权限
#### 火山引擎 Bio-OS
账号的AK/SK需要具有数据所在对象存储TOS的读写权限以及Bio-OS的使用权限。
#### 功能列表
1. config 配置平台AS/SK和endpiont
2. create-workflow 将Gitee中的WDL工作流导入
3. create-submission 批量投递工作流任务
4. get-submission 查询批量投递工作流任务状态
5. list-workflows 查询工作空间中的WDL工作流
6. list-runs 查询投递任务的运行详情
7. list-workspaces 查询拥有的工作空间
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