April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
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第
10
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Could not build the path
"gs://genomics-in-the-cloud/v1
/data/germline/intervals/snippet-intervals-min.list". It
may refer to a filesystem not supported by this instance of
Cromwell. Supported filesystems are: HTTP, LinuxFileSystem.
上述信息表明，
Cromwell
默认无法将
GCS
当作输入文件的源头，即使它在
GCP
平台上运行一个虚拟机实例。这就是为什么我们前面使用的配置文件明确
指定支持
GCS
文件系统：
filesystems {
gcs {
文件系统声明出现在两个位置：分别在最顶层的
engine
和
backend
块。
engine
块中的声明指定
Cromwell
引擎解释
WDL
脚本时，自身可拉取
GCS
中的文件。
我们的示例需要这个配置，因为引擎必须从
GCS
检索片段列表，以便处理分
发命令。而
backend
块中的声明使得通过
PAPI
执行的调用命令可使用
GCS
中
的文件。
原则上讲，你可以创建一种混合式配置，用本地系统执行，但可以将
GCS
作
为一种可支持的文件系统。但需注意的是，这将导致
Cromwell
将这些文件的
副本放到实例的本地存储。如在
GCP
以外的地方用这种配置运行工作流，你（或
桶的所有者）将被收取下行流量费。如大规模数据处理，使用该方式的成本很高。
10.2.3 ...
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I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.