構建基于docker的基因數據分析應用生態系統（33頁）.pdf

1、 docker in Bio/informatics署名：黃澤輝職稱：華大基因互聯網產品總監構建基因數據應用生態系統構建基因數據應用生態系統一、基因組學數據與分析應用二、存在的問題與挑戰三、Docker與應用標準化四、如何構建基因“App Store”目 錄content一、基因組學數據與分析應用ExpressionStructurePhenotypeSequenceInteractions二、存在的問題與挑戰http:/ of software and hardware environmentsfrom workstations to cluster,cloud,and high perfo

2、rmance computing(HPC)environments.version control三、Docker與應用標準化1.使用預配置docker鏡像提供運行時環境-輕量化-簡單易用-穩定可重復-不區分開發語言和操作系統-版本化控制2.統一的CLI（執行）描述語言-Tool Wrapper/Tool specification-Linked-Data-兼容POSIX標準3.統一流程（DAG）描述語言-使用工具或者子流程構建流程-定義任務依賴關系-數據Streaming-任務并行-動態生成作業4.提供完整的工具鏈（support tooling）-工具開發（author）-調試（debug

3、）-運行（scheduler）4.利用Dockerfile&Docker Registry分發軟件-簡便的分發和使用-Dockerfile構建鏡像DockstoreA tool consists of:a(currently Docker)image a document that describes how to use that image(currently CWL or WDL)a Dockerfile that describes how to re-produce the image in the future四、如何構建基因“App Store”UserDeveloperDock

4、erfileTool.cwlBuild SystemDocker ImageApp StoreworkloadJSON parameterization fileGA4GH-compliant workflow execution service.Eclipse Che-在線開發工具Visual editorTool registry apiWorkflow execution api-ability to request a workflow run using CWL or WDL(and maybe future formats)-ability to parameterize that workflow using a JSON schema thats simple and used in common between CWL and WDL-ability to get information about running workflows,status,errors,output file locations etc