生物資訊計算平台＆工具
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###### 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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