Parabricks 軟體下載＆安裝說明 === ###### tags: `Parabricks-v3.5` ###### tags: `基因體`, `NVIDIA`, `Clara`, `Parabricks`, `二級分析` > 這裡的 Parabricks 是指 Parabricks Pipeline 工具 <br> [TOC] <br> :::warning :information_source: **[HACKMD] Parabricks 2.5 & 3.1 的舊版資訊** - [NVIDIA / Parabricks / 軟體下載與安裝(v1)](/jbvnEl5YRwWBa3QMGBcHbQ) ::: <br> ## [官方文件（v3.5）](https://docs.nvidia.com/clara/parabricks/v3.5/index.html) :::warning :information_source: **入口點** https://docs.nvidia.com/clara/#parabricks ![](https://i.imgur.com/KR0HXTL.png =50%x) ::: - [[概要][PDF] NVIDIA CLARA PARABRICKS PIPELINES FOR GENOMICS ANALYSIS](https://resources.nvidia.com/c/healthcare-genomics-?x=sFVHf4&lx=OhKlSJ&topic=Solution%20Brief) [![](https://i.imgur.com/W96hKlW.png)](https://i.imgur.com/W96hKlW.png) [![](https://i.imgur.com/lxQsSBs.png)](https://i.imgur.com/lxQsSBs.png) <br> <hr> <br> ## 下載 Parabricks 安裝套件 ### Step1 - 填寫申請表格 - ### https://www.nvidia.com/en-us/docs/nvidia-parabricks-general/ ![](https://i.imgur.com/47NaFwa.png) - ### 使用 gmail 帳號申請，收到的信件有可能跑到促銷廣告裡 ![](https://i.imgur.com/Kh0y5Q6.png) - ### 在接下來的 72 小時內，可取得 license key ![](https://i.imgur.com/eYInq5a.png) <br> ### Step2 - 審核通過，接著註冊 Nvidia 帳號 ![](https://i.imgur.com/6gvi70J.png) - → [**SIGN IN TO NVIDIA GPU CLOUD**](http://tmailclick.nvidia.com/track/click/30646027/ngc.nvidia.com?p=eyJzIjoiemk4a0ZzYjBSZDBoR3FkVzRRSVVDY3M0cUdBIiwidiI6MSwicCI6IntcInVcIjozMDY0NjAyNyxcInZcIjoxLFwidXJsXCI6XCJodHRwczpcXFwvXFxcL25nYy5udmlkaWEuY29tXFxcL3NpZ25pblwiLFwiaWRcIjpcIjY3NTExNDU4ZGZjNTQyZDViMDlhMzhmOGY5MDMzNDllXCIsXCJ1cmxfaWRzXCI6W1wiOTMyMjA0ZTc3NjA5ZDY4MzNkN2JjYzQ5MTI4YzI4OTdlMWU2OGFiNFwiXX0ifQ) - 必須使用 Step1 申請的 email，去註冊為 Nvidia 帳號，這樣才看的到資源。 也就是說，權限 `external-parabricks-trial-users` 是綁定到該 email - 有權限情況下，在註冊後，可以看到 `parabricks_free_trial` 資源 ![](https://i.imgur.com/cshDocl.png) - 沒有權限情況下，看不到資源 ![](https://i.imgur.com/dBBV5gB.png) <br> ### Step3 - 下載 license key [![](https://i.imgur.com/dwhlOde.png)](https://i.imgur.com/dwhlOde.png) - ### [Here](https://ngc.nvidia.com/resources/external-parabricks-trial-users:parabricks_free_trial) is a link to the trial license resource. - https://ngc.nvidia.com/resources/external-parabricks-trial-users:parabricks_free_trial ![](https://i.imgur.com/bdA0KM2.png) 這一頁是用來下載 license key - ### [Here](https://forums.developer.nvidia.com/uploads/short-url/5kvnj7M9EiMH70vInNOHsj3GOiM.pdf) are the download instructions. - https://forums.developer.nvidia.com/uploads/short-url/5kvnj7M9EiMH70vInNOHsj3GOiM.pdf 這個 link 則是 pdf 教學文件，教導如何下載 license key - ### 下載方法有 3 種 (請查看 pdf) 1. 直接點選「資源清單入口」的下載點 ==(不 work)== ![](https://i.imgur.com/4U8On0T.png) 2. 進入「parabricks_free_trial 資源」，從 File Browser 點選下載 ![](https://i.imgur.com/y8B9FME.png) - https://ngc.nvidia.com/resources/external-parabricks-trial-users:parabricks_free_trial/files?version=3.7.0-1_2022-05-31# - https://ngc.nvidia.com/resources/external-parabricks-trial-users:parabricks_free_trial/files?version=3.7.0-1_2022-08-31 3. 進入「parabricks_free_trial 資源」，執行 CLI command ==(不 work)== 1. 需事先安裝 CLI 2. 取得 API key 3. 執行 ngc 指令 (CLI command) 註：CLI command 主要是給終端機使用 - ### 亦可在論壇下載教學文件 https://forums.developer.nvidia.com/t/how-to-download-clara-parabricks-pipelines-trial-version/165217 ![](https://i.imgur.com/ik2VrpV.png) - ### 下載的 license key 長相 ``` parabricks.tar.gz ├── [ 793] Dockerfile_post ├── [2.4K] Dockerfile_post_extra_tools ├── [ 32K] EULA.txt ├── [ 24K] installer.py <--- pbrun 安裝程式 ├── [ 697] installMantaAndStrelka.sh ├── [ 181] license.bin <--- license key ├── [ 698] singularity_post └── [1.6K] singularity_post_extra_tools ``` <br> <hr> <br> ## [補充說明] 下載 license key ### 透過 CLI command :::info :bulb: 關於 Ubuntu20.04 (2022/03/04 補充) - [Account > Setup](https://ngc.nvidia.com/setup) - [CLI](https://ngc.nvidia.com/setup/installers/cli) - AMD64 Linux: 執行檔可執行 ``` $ ngc usage: ngc [--debug] [--format_type <fmt>] [--version] [-h] {config,diag,registry} ... ngc: error: too few arguments ``` - ARM64 Linux: 執行檔不可執行 ``` $ ngc bash: ./ngc: cannot execute binary file: Exec format error ``` - [Generate API Key](https://ngc.nvidia.com/setup/api-key) ::: - - 2021/06/04 - 操作指令(沒有成功) ``` $ ngc config set $ docker login nvcr.io $ ngc registry resource download-version \ "external-parabricks-trial-users/parabricks_free_trial:v3.5.0_2021-07-31" ``` [![](https://i.imgur.com/t7LeNtm.png)](https://i.imgur.com/t7LeNtm.png) [![](https://i.imgur.com/fhnZsle.png)](https://i.imgur.com/fhnZsle.png) - 2022/03/04 - 有成功，可以 work ``` $ ngc config set Enter API key [no-apikey]. Choices: [<VALID_APIKEY>, 'no-apikey']: N29******************************************************************************DBk Enter CLI output format type [ascii]. Choices: [ascii, csv, json]: json Enter org [no-org]. Choices: ['ea-nvidia-clara-train', 'external-parabricks-trial-users']: 'external-parabricks-trial-users' { "error": "Invalid org. Please re-enter." } Enter org [no-org]. Choices: ['ea-nvidia-clara-train', 'external-parabricks-trial-users']: external-parabricks-trial-users Enter team [no-team]. Choices: ['no-team']: Enter ace [no-ace]. Choices: ['no-ace']: ``` ```bash $ docker login nvcr.io Username: $oauthtoken Password: WARNING! Your password will be stored unencrypted in /home/tj/.docker/config.json. Configure a credential helper to remove this warning. See https://docs.docker.com/engine/reference/commandline/login/#credentials-store Login Succeeded ``` ```json $ ngc registry resource download-version "external-parabricks-trial-users/parabricks_free_trial:3.7.0-1_2022-05-31" { "download_end": "2022-03-04 13:01:21.155012", "download_start": "2022-03-04 13:01:17.149735", "download_time": "4s", "files_downloaded": 1, "local_path": "/home/tj/Downloads/parabricks_free_trial_v3.7.0-1_2022-05-31", "size_downloaded": "20.16 KB", "status": "Completed", <----- "transfer_id": "parabricks_free_trial_v3.7.0-1_2022-05-31" } ``` <br> <hr> <br> ## 安裝說明 :::warning :bulb: 先行了解，再上機操作 ::: ### [Step1 - 前置作業：檢查執行環境](https://docs.nvidia.com/clara/parabricks/v3.5/text/getting_started.html#step-1-make-sure-installation-requirements-are-met) - `>=` cuda-10.0 - nvidia-docker - python3 - curl - 單顆 GPU 的記憶體，至少要 12GB 以上 - GPU 配置 | GPU num | CPU RAM | CPU threads| | ------- | ------- | ---------- | | 1 | 50GB ? | 16 | | 2 | 100GB | 24 | | 4 | 196GB | 32 | | 8 | 392GB | 48 | - [透過 pbrun 參數](https://docs.nvidia.com/clara/parabricks/v3.5/text/germline_pipeline.html) - ```--num-gpus NUM_GPUS``` Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used. If you are using flexera, please include –gpu-devices too. - 單顆 GPU 至少要 16 條執行緒 ``` WARNING The system has 12 threads, however recommended number of threads with 1 GPU is 16. The run might not finish or might have less than expected performance. ``` - 單顆 CPU 也可完成 Germline | Time | Function | | ---- | -------- | | 5m 50s | GPU-BWA mem, Sorting Phase-I | | 0m 10s | Sorting Phase-II | | 2m 02s | Marking Duplicates, BQSR | | 6m 45s | GPU-GATK4 HaplotypeCaller | | **14m 47s** | **Total** | <br> ### [Step2 - 下載 parabricks 套件](https://docs.nvidia.com/clara/parabricks/v3.5/text/getting_started.html#step-2-downloading-installation-package) - 就是 parabricks.tar.gz 那包 <br> ### [Step3 - 安裝 parabricks 套件](https://docs.nvidia.com/clara/parabricks/v3.5/text/getting_started.html#step-3-install-the-parabricks-suite) <br> ### [Step4 - 下載測試樣本，並執行工具](https://docs.nvidia.com/clara/parabricks/v3.5/text/getting_started.html#step-4-example-run) <br> <hr> <br> ## 一些重點資訊 - [What is CLARA PARABRICKS Pipelines?](https://docs.nvidia.com/clara/parabricks/v3.5/text/software_overview.html#what-is-clara-parabricks-pipelines) - Parabricks 是軟體套件，執行二級分析 - 主要優點：速度極快、低成本 - 30x WGS 資料，傳統約需 30 小時，Parabricks 只需 45 分 - [SOFTWARE OVERVIEW](SOFTWARE OVERVIEW) - NEW [![](https://i.imgur.com/2md6GPy.png)](https://i.imgur.com/2md6GPy.png) - OLD [![](https://i.imgur.com/AyMBNKQ.png)](https://i.imgur.com/AyMBNKQ.png) - 差異 1. 舊的 [RNA] alignment 併到 [ALIGNMENT] 2. [PREPROCESSING] BWA Mem Alignment 換成 [MerBam] <br> <hr> <br> ## 一些新的資訊 ### 文件整個大翻修 - 針對不同版本工具，對應到不同份文件 - 流程圖圖片也都重新翻修 ### Pipeline - 示意圖 [![](https://i.imgur.com/voJnXjF.png)] [PDF](https://cf-store.widencdn.net/nvdam/e/d/8/ed89685e-4e84-449f-bd83-bc0ff92e4180.pdf?response-content-disposition=attachment%3B%20filename%3D%22Parabricks%20Pipelines%20Updated%20Data%20Sheet.pdf%22&Expires=1625115735&Signature=JhVZTu8xLcSIBAAyLPkPreDlSLZ4X00NUew70iyL3J3EHp0-~K6yf3rHXz4FZPsBCt5Il05NySRxDpfIPJvW9OAx0YJHr7y9gEwVWD~D0ZrJwmchufm2Ade5vgqA2OgHwBtn3xQQ0INgE2fLdCpZFW3WOeY4K7ZnPveGMAuICDtRva4f2S7ukcxied0ZYzc3KiiNUKvbS3MnZzJ65dsrfvWXeTMbEGYBirasuAz1JKB2KDUlpR2Rx7ky7rckBDBhZtY8A8awqCaMue3CGMDrZa5dDbIgK~apRYdr4Y9x8Z~U-T80fwfls1JQkAwfDRV4~oU4sbupXI~3G0z7wMjlrg__&Key-Pair-Id=APKAJD5XONOBVWWOA65A) ([資料來源](https://resources.nvidia.com/c/healthcare-genomics-?x=sFVHf4&lx=OhKlSJ&topic=Solution%20Brief)) - 新增 [DEEPVARIANT GERMLINE PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.5/text/deep_pipeline.html#rst-deep) - 但沒有提供 pipeline 指令 - 過去是用 fq2bam + deepvariant 兩個單一工具組裝 - **GERMLINE** vs. **DEEPVARIANT GERMLINE** - GERMLINE [![](https://i.imgur.com/fQucTgf.png)](https://i.imgur.com/fQucTgf.png) - DEEPVARIANT GERMLINE [![](https://i.imgur.com/iftYYS0.png)](https://i.imgur.com/iftYYS0.png) - 新增 [RNA PIPELINE](https://docs.nvidia.com/clara/parabricks/v3.5/text/rna_pipeline.html#rst-rna) - **GERMLINE** vs. **RNAseq** - GERMLINE [![](https://i.imgur.com/fQucTgf.png)](https://i.imgur.com/fQucTgf.png) - RNAseq [![](https://i.imgur.com/aAThMud.png)](https://i.imgur.com/aAThMud.png) - 參考資料 - [BWA or STAR for RNAseq?](https://www.biostars.org/p/330942/) > Q: 為何不使用 BWA 就好了，要用 STAR 映射到參考框架? > A: BWA 不會認知到有剪接，除非你正在處理的是沒有內含子的細菌 - [比对软件STAR的简单使用](https://www.bioinfo-scrounger.com/archives/288/) - [【生信小课堂】如何直观的理解RNA-seq分析流程](https://zhuanlan.zhihu.com/p/139773946) :+1: - [生物信息学流程：mRNA Analysis Pipeline](https://www.jianshu.com/p/b0d3a24e349e) - [最新版针对RNA-seq数据的GATK找变异流程](https://cloud.tencent.com/developer/article/1536221) - [STAR-Fusion 寻找融合基因](https://www.sohu.com/a/396207045_652735) <br> ## 參考資料 - [TWCC Parabricks Quickstart & Tutorial](https://hackmd.io/@kmo/twcc_hpc_parabricks)