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README.md
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| > | > | ||||
| > Email: [qwch20@fudan.edu.cn](mailto:qwch20@fudan.edu.cn) | > Email: [qwch20@fudan.edu.cn](mailto:qwch20@fudan.edu.cn) | ||||
| > | > | ||||
| > Last Updates: 18/08/2021 | |||||
| > Last Updates: 22/08/2021 | |||||
| #### Brief Introduction | #### Brief Introduction | ||||
| $ source activate choppy (open-choppy-env) | $ source activate choppy (open-choppy-env) | ||||
| # 第一次安装 | # 第一次安装 | ||||
| $ choppy install chenqingwang/SplAdder-merge | |||||
| $ choppy install chenqingwang/SplAdder-merge-T | |||||
| # 非第一次安装 | # 非第一次安装 | ||||
| $ choppy install chenqingwang/SplAdder-merge -f | |||||
| $ choppy install chenqingwang/SplAdder-merge-T -f | |||||
| # 查询已安装APP | # 查询已安装APP | ||||
| $ choppy apps | $ choppy apps | ||||
| ``` | ``` | ||||
| # 准备 samples.csv 文件 | # 准备 samples.csv 文件 | ||||
| $ choppy samples chenqingwang/SplAdder-merge-latest > samples.csv | |||||
| $ choppy samples chenqingwang/SplAdder-merge-T-latest > samples.csv | |||||
| # 准备无默认参数的samples.csv 文件 | # 准备无默认参数的samples.csv 文件 | ||||
| $ choppy samples --no-default chenqingwang/SplAdder-merge-latest > samples.csv | |||||
| $ choppy samples --no-default chenqingwang/SplAdder-merge-T-latest > samples.csv | |||||
| # 提交任务 | # 提交任务 | ||||
| $ choppy batch chenqingwang/SplAdder-merge-latest samples.json -p Your_project_name -l Your_label | |||||
| $ choppy batch chenqingwang/SplAdder-merge-T-latest samples.csv -p Your_project_name -l Your_label | |||||
| # 查询任务运行状况 | # 查询任务运行状况 | ||||
| $ choppy query -L Your_label | grep "status" | $ choppy query -L Your_label | grep "status" | ||||
| $ oss://choppy-cromwell-result/test-choppy/Your_project_name/ | $ oss://choppy-cromwell-result/test-choppy/Your_project_name/ | ||||
| ``` | ``` | ||||
| #### Input File | |||||
| Input file samples.json should be in the form of json. For example: | |||||
| #### Description | |||||
| ``` | ``` | ||||
| { | |||||
| "bam": [ | |||||
| "oss://choppy-cromwell-result/test-choppy/..._xxx.bam", | |||||
| "oss://choppy-cromwell-result/test-choppy/..._xxx.bam", | |||||
| "oss://choppy-cromwell-result/test-choppy/..._xxx.bam" | |||||
| ], | |||||
| "bai": [ | |||||
| "oss://choppy-cromwell-result/test-choppy/..._xxx.bai", | |||||
| "oss://choppy-cromwell-result/test-choppy/..._xxx.bai", | |||||
| "oss://choppy-cromwell-result/test-choppy/..._xxx.bai" | |||||
| ], | |||||
| "pickle": [ | |||||
| "oss://choppy-cromwell-result/test-choppy/..._xxx.pickle", | |||||
| "oss://choppy-cromwell-result/test-choppy/..._xxx.pickle", | |||||
| "oss://choppy-cromwell-result/test-choppy/..._xxx.pickle" | |||||
| ], | |||||
| "sample_id": "B13150xx" | |||||
| } | |||||
| ``` | |||||
| PS: sample_id is necessary for Choppy system | |||||
| # samples: The file names to be analyzed should be written line by line in this file, and the file should be uploaded to AliCloud. | |||||
| ``` |
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