在Wellcome Trust Sanger Institute使用病原体管道的工具
path_pipe_conf_tools的Python项目详细描述
这可能不是很有趣除非你研究病原体 威康信托桑格研究所的信息学团队 当然不是你不使用the vr-pipe pipeline。
给定一个配置目录，此脚本将查找 *_pipeline.conf目录中的文件及其直接子级。 它解析这些文件并以json格式输出其内容。这不是 保存到文件或标准输出。
这是与 jsontoemail和 cron向病原体信息学发送更新/提醒的作业 团队。
用法
$ list-pathogen-pipeline-jobs -h
usage: list-pathogen-pipeline-jobs [-h] [--output_file OUTPUT_FILE] config_dir
Outputs details of all of the pathogen jobs in the pipeline
positional arguments:
config_dir Config directory to be searched for job trackers (also
searches child dircectories)
optional arguments:
-h, --help show this help message and exit
--output_file OUTPUT_FILE, -o OUTPUT_FILE
File to output results to (defaults to stdout)
示例输出
{
"created_at": "2015-03-24T15:26:17.246253",
"jobs": [
{
"approval_required": true,
"config_file": "/parent_dir/assembly_jobs/job_1.conf",
"job_type": "__Assembly__",
"pipeline_tracker": "/parent_dir/assembly_job_tracker.conf"
},
{
"approval_required": true,
"config_file": "/parent_dir/assembly_jobs/job_2.conf",
"job_type": "__Assembly__",
"pipeline_tracker": "/parent_dir/assembly_job_tracker.conf"
},
{
"approval_required": false,
"config_file": "/parent_dir/assembly_jobs/job_3.conf",
"job_type": "__Assembly__",
"pipeline_tracker": "/parent_dir/assembly_job_tracker.conf"
},
{
"approval_required": true,
"config_file": "/parent_dir/annotation_jobs/job_1.conf",
"job_type": "__Annotation__",
"pipeline_tracker": "/parent_dir/annotation_job_tracker.conf"
},
{
"approval_required": false,
"config_file": "/parent_dir/mapping_jobs/job_1.conf",
"job_type": "__Mapping__",
"pipeline_tracker": "/parent_dir/mapping_job_tracker.conf"
},
{
"approval_required": false,
"config_file": "/parent_dir/mapping_jobs/job_2.conf",
"job_type": "__Mapping__",
"pipeline_tracker": "/parent_dir/mapping_job_tracker.conf"
}
]
}
测试
./run_tests.sh
依赖关系
测试要求：
- 模拟
path_pipe_conf_tools已经用python在ubuntu 12.04上测试过了 2.7.3
欢迎加入QQ群-->： 979659372
