GATK资源包下载攻略及详细教程

由于从Google Buckets和FTP下载GATK Resource Bundle变得不便，目前只能通过Azure进行下载。本文详细介绍了如何从Azure下载GATK Resource Bundle的步骤，包括资源地址的获取和azcopy工具的使用。通过访问GATK官网和Azure相关页面，可以找到五种不同资源的下载地址，并通过azcopy工具实现高效下载。

由于众所周知的原因，从Google Buckets下载GATK Resource Bundle并不容易，而FTP下载方式自2020年起已关闭，目前只剩下通过Azure下载这一种方法。以下是如何从Azure下载GATK Resource Bundle的详细步骤。

根据GATK官网关于Resource bundle的说明（https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle），Azure中的GATK Resource Bundle资源地址可以在GATK Resource Bundle（https://learn.microsoft.com/en-us/azure/open-datasets/dataset-gatk-resource-bundle）中找到。重点关注的是各种Resource bundle的Data Access地址：

datasetgatkbestpractices
West US 2: 'https://datasetgatkbestpractices.blob.core.windows.net/dataset'
West Central US: 'https://datasetgatkbestpractices-secondary.blob.core.windows.net/dataset'
SAS Token: ?sv=2020-04-08&si=prod&sr=c&sig=6SaDfKtXAIfdpO%2BkvNA%2FsTNmNij%2Byh%2F%2F%2Bf98WAUqs7I%3D
<p>datasetgatklegacybundles
West US 2: '<a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero55fZW9jH_QnKrIoZytpKO8iZScvmykmZSQbqPHqryygJ-B2MZmetmRlZ2ykrllY8OJZZ_HbJyqfKZupMmmn6ONionNx2aHlIHcsaOB336bvIaBaLJ9ipx_jYujss2ra42fhN6ziJiZh6q5s4aYfaqvZIVlvrOSmn-KdnU' rel='nofollow'>https://datasetgatklegacybundles.blob.core.windows.net/dataset</a>'
West Central US: '<a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero55fZW9jH_QnKrIoZytpKO8iZScvmykmZSQbqPHqryygIqF0b1matmSqqqynbllmcR5aZ2xpoamk6aOrcmV0q2OeXCYx61m2ZK7ta-SrXZgu4p-oMl8hZp5soaiv6q7aIN2eJW-iJyUkqetsYaYepqvnJtotI2gnH2znaKy3bSkgomEl72unKE' rel='nofollow'>https://datasetgatklegacybundles-secondary.blob.core.windows.net/dataset</a>'
SAS Token: ?sv=2020-04-08&si=prod&sr=c&sig=xBfxOPBqHKUCszzwbNCBYF0k9osTQjKnZbEjXCW7gU0%3D</p><p>datasetgatktestdata
West US 2: '<a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero55fZW9jH_QnKrIoZytpGC8in5kv4B-YImMbqHHqp-hgJ-F28ehhtmcldCukq1pY8WrZam_kYmmioB_aL67tKSYdYTPra1-zpKquWmHqnFgvIabZL99gah-a4Oiss3RbIOGn9GxrpXOhd2ypYa9fWK7rJtx' rel='nofollow'>https://datasetgatktestdata.blob.core.windows.net/dataset</a>'
West Central US: '<a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero55fZW9jH_QnKrIoZytpGC8in5kv4B-YImMarK_urSulp-JzceinNmR0Nyvkc9lmsRleqCxp5ygkqaLrsmWs62Wn42VsGaDzJyqqrOSvoGaq6t9nq5ripx-faCvs6q7bYJ5iN6xiJXNkd2tboeqm2S8hn1nvrOFqoqNj6Kz0LNt' rel='nofollow'>https://datasetgatktestdata-secondary.blob.core.windows.net/dataset</a>'
SAS Token: ?sv=2020-04-08&si=prod&sr=c&sig=fzLts1Q2vKjuvR7g50vE4HteEHBxTcJbNvf%2FZCeDMO4%3D</p><p>datasetpublicbroadref
West US 2: '<a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero55fZW9jH_QnKumapHTqKC7ZHqtx2t-m5Omj6Wx0LCrlmSA2r1mat2Stplsmb1lm8RllK6xpm2clHxyo767uKCXZI2Vra1-zoHcsqSSuoFkr3aCoLSNipt9o35rvtCzsYOGnpqze4behpWxs4WYhWG7rIqetIp1bQ' rel='nofollow'>https://datasetpublicbroadref.blob.core.windows.net/dataset</a>'
West Central US: '<a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero55fZW9jH_QnKumapHTqKC7ZHqtx2t-m5Omj6Wxu7SkjWRw2r57d92dtpmimq1pma6ffqrIpo2llGulrb-qn2uXq2zavoyC2pKqqmmRvn6cxnV9nq6yhZqKgI5otKenaI6GopW-eHrchpWuo4XQm2SxhpigsrOcmn2zh6SzurNqjayiog' rel='nofollow'>https://datasetpublicbroadref-secondary.blob.core.windows.net/dataset</a>'
SAS Token: ?sv=2020-04-08&si=prod&sr=c&sig=DQxmjB4D1lAfOW9AxIWbXwZx6ksbwjlNkixw597JnvQ%3D</p><p>datasetbroadpublic
West US 2: '<a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero55fZW9jH_QnKquspqYdpvFeoadx4Ckmnymg6vHla-tjWRw3r6HZpeZupmkmpmUqq6fZaDJfHGbiZGLoMiVvGh9q4TPra1_z5K3tW2FqoKcsYaCn7KjfWOJpoaxtLfNbYN5jN-yZn7ehZW5apHgipqxg21x' rel='nofollow'>https://datasetbroadpublic.blob.core.windows.net/dataset</a>'
West Central US: '<a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero55fZW9jH_QnKquspqYdpvFeoadx4CkmnyRh6S-lZ-tjnl93smHZs2aqp2ihNN-psWfhanJa6SlioBya8jcm62Oiojbvnt3lJG7sqWcqX2aq6t9nr-AjWB_fXpov7fRaI52gN2yZnvOhc3PbYe6mJyvrJSesrOGnH6Qhmq-3dF1' rel='nofollow'>https://datasetbroadpublic-secondary.blob.core.windows.net/dataset</a>'
SAS Token: ?sv=2020-04-08&si=prod&sr=c&sig=u%2Bg2Ab7WKZEGiAkwlj6nKiEeZ5wdoJb10Az7uUwis%2Fg%3D</p>

可以看到共有5种资源可供下载，他们的具体解释可参见GATK resource bundle官网。每一种资源有两个服务器地址，分别是West US 2地址和West Central US地址，同时还给出了token值，只需将两者合并在一起即可得到一个合法的Azure资源地址。

为了从Azure下载数据，需要使用azcopy工具。azcopy的安装与使用详情见（https://learn.microsoft.com/en-us/azure/storage/common/storage-use-azcopy-v10）。以下以Linux版本的azcopy为例，下载datasetgatklegacybundles资源。

首先，下载并安装azcopy：

wget <a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero2Jq82woWLehJW2r5yYZaPEZHafvpGompJse22xu7-wgXVo2MWLZpWdprGjgd99mrx5hWS0fXlgio2kaL-nr7CCZIHPsZ6cmIe3zKWF4JSar6x-oLOQhWKJs6R1' rel='nofollow'>https://aka.ms/downloadazcopy-v10-linux</a>
mv downloadazcopy-v10-linux az-copy.tar
tar -xvf az-copy.tar<h1>将azcopy添加到PATH中</h1><h1>echo 'export PATH=$PATH:you_azcopy_path' >> ~/.bashrc</h1><h1>source ~/.bashrc</h1>

接下来，将datasetgatklegacybundles的资源地址拼接好：

# West US 2<p>gatklegacybundles_http_1='<a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero55fZW9jH_QnKrIoZytpKO8iZScvmykmZSQbqPHqryygJ-B2MZmetmRlZ2ykrllY8OJZZ_HbJyqfKZupMmmn6ONionNx2aHlIiWsmuIunmnr5xxqLJ9iaR9faClvrqXr4NkfdnHeKXembeVsJvTaZusn3aoyH2smJKRem_Ilq9xjauRzcaMcpuRupWwh5l-oLysYWi2ppJkhGp7e8i4zoSKh4XfyaKhl5HOmX2J0px3r3mjacdshoWFkKmEx8_WoYaJp761ZZSXkpS5sIK6fnWrq32errKGm4qNimyyp7ikg4aJ0LGedpeR0LGyh7qXZbF5ha6za4WqfWuOab7dwKKDg3Si' rel='nofollow'>https://datasetgatklegacybundles.blob.core.windows.net/dataset?sv=2020-04-08&amp;si=prod&amp;sr=c&amp;sig=xBfxOPBqHKUCszzwbNCBYF0k9osTQjKnZbEjXCW7gU0%3D</a>'</p><h1>West Central US</h1><p>gatklegacybundles_http_2='<a target='_blank'  href='https://www.17golang.com/gourl/?redirect=MDAwMDAwMDAwML57hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Juaq6t9nq5roGCUgXuytMyero55fZW9jH_QnKrIoZytpKO8iZScvmykmZSQbqPHqryygIqF0b1matmSqqqynbllmcR5aZ2xpoamk6aOrcmV0q2OeXCYx61m2ZK7ta-SrXZgu4p-oMl9caqUo2mxsqevr4CGeJWwiHKYgtCqrZuqpJjEinFryGujaZOBg66_psCglop4nL2LYtuHlrKyiL19nbuJYau0a36kk32tssa6yXGZd4HSyXlqtYnRqoKLl4Z0xWWgaslrgn-BaYOSt82oqoOJcN-6enfVi5WZmpHRhqG5d36Ms2uchn18jrK3prOifauEz757hpSHp6VpkrqbYLx2eayza4KafaOkbLS3zqSBrJvPsa5_0Ia6sWuR4Jtt' rel='nofollow'>https://datasetgatklegacybundles-secondary.blob.core.windows.net/dataset?sv=2020-04-08&amp;si=prod&amp;sr=c&amp;sig=xBfxOPBqHKUCszzwbNCBYF0k9osTQjKnZbEjXCW7gU0%3D</a>'</p>

然后，使用azcopy下载资源：

# azcopy copy [source] [destination] [flags]
azcopy copy $gatklegacybundles_http_1 gatklegacybundles --recursive

由于这是文件夹下载，记得要加上--recursive参数，然后就可以等待资源下载就绪了。

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