bam-readcount/README.md

### README.md

> Author: Qingwang Chen
>
> Email: qwch20@fudan.edu.cn
>
> Last Updates: 16/10/2020

#### Requirements

- choppy
- Ali-Cloud
- Linux

```
# 激活choppy环境
$ source activate choppy (open-choppy-env)

# 第一次安装
$ choppy install chenqingwang/bam-readcount
# 非第一次安装
$ choppy install chenqingwang/bam-readcount -f 

# 查询已安装APP
$ choppy apps
```

#### Quick Start

```
# 准备 samples.csv 文件
$ choppy samples junshang/bedtools-latest > samples.csv

# 提交任务
$ choppy batch junshang/bedtools-latest samples.csv -p Your_project_name -l Your_label

# 查询任务运行状况
$ choppy query -L Your_label | grep "status"

# 查询失败任务
$ choppy search -s Failed -p Test_bamreadcount_chenqingwang_20201016 -u chenqingwang --short-format

# 结果文件地址
$ oss://choppy-cromwell-result/test-choppy/Your_project_name/
```