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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 chenqingwang/bam-readcount-latest > samples.csv
# 提交任务
$ choppy batch chenqingwang/bam-readcount-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/