---
# System prepended metadata

title: 生物資訊計算平台＆工具
tags: [', 生物資訊計算工具', 生物資訊]

---

生物資訊計算平台＆工具
===
###### tags: `生物資訊`
###### tags: `生物資訊`, 生物資訊計算平台`, 生物資訊計算工具`

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## [Overall] 研究看看：尋找適合作為「生物資訊計算工具」的套件
- [Accelerating Analytics for the Future of Genomics](https://www.slideshare.net/AmazonWebServices/accelerating-analytics-for-the-future-of-genomics)
    > Page44: 有個 runtime {}, 可以設定執行時所需要的環境與參數
    > https://cromwell.readthedocs.io/en/stable/RuntimeAttributes/
    > 
    > https://cromwell.readthedocs.io/en/stable/backends/Backends/
    > Cromwell 支援的 backend
    > 有 HPC, GA4GH TES, Spark
    >  
    > 不同 backend 支援的 runtime 參數會有所不同,
    > 例 Spark 支援的 runtime attributes 是
    >  
    > - executorCores (default value is 1)
    > - executorMemory (default value is "1GB", Unit in MB or GB or TB.. )
    > - appMainClass ( Spark app/job entry point)
    > - numberOfExecutors ( Specific to cluster deploy mode)
    > - additionalArgs ( i.e to add additional configuration or parameters to spark-submit)
- Cromwell
    - 概念
        > cromwell 就是
        > 透過 cromwell server 去 submit job 給 batch service
        > 再透過 batch service 去執行 job
    
    - [在 AWS 中国区域一键部署面向基因分析的 Cromwell-on-AWS-Batch 解决方案
](https://aws.amazon.com/cn/blogs/china/one-click-deployment-of-cromwell-on-aws-batch-solution-for-genetic-analysis-in-aws-china/)
        > Cromwell 是由Broad研究院面向科研领域开发的一套工作流管理框架，目前在基因分析领域更为常用。
    - [[AWS] AWS Batch 初體驗](https://medium.com/bryanyang0528/aws-batch-%E5%88%9D%E9%AB%94%E9%A9%97-4a19485d2318)
- Microsoft - Genomics
    [Accelerate precision medicine with Microsoft Genomics](https://azure.microsoft.com/mediahandler/files/resourcefiles/accelerate-precision-medicine-with-microsoft-genomics/Accelerate_precision_medicine_with_Microsoft_Genomics.pdf)
- WDL
    - [broadinstitute/wdl-runner example](https://github.com/broadinstitute/wdl-runner/tree/master/wdl_runner)
    - [标准流程描述语言 WDL 阿里云最佳实践](https://developer.aliyun.com/article/716546)
- Nextflow
- DeepChem

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