用于从basemount检索文件的内部bfssi包
BaseMountRetrieve的Python项目详细描述
基本安装检索
用于在本地miseq运行的输出样式中从basemount检索文件的包。
输出目录示例
Project
├── 20180714_WGS_M01308
│ ├── Config
│ ├── Data
│ │ └── Intensities
│ │ └── BaseCalls
│ ├── Images
│ ├── InterOp
│ ├── Logs
│ ├── Recipes
│ └── Thumbnail_Images
└── 20181102_WGS_M01308
├── Config
├── Data
│ └── Intensities
│ └── BaseCalls
├── Images
├── InterOp
├── Logs
├── Recipes
└── Thumbnail_Images
要求
- BaseMount（确认支持的版本：illumina basemount v0.15.96.2154）
- python 3.6
安装
pip install basemountretrieve
使用量
Usage: basemountretrieve [OPTIONS]
BaseMountRetrieve will tap into the mounted BaseMount filesystem and
retrieve all of the runs for a given project in the output style of a
local MiSeq run.
Options:
-p, --project-dir PATH Path to the directory on BaseMount for a
particular project. e.g.
basemount/Projects/[your project].
-e, --experiment-name TEXT Searches BaseMount for the name of a
run/experiment and attempts to retrieve its
contents. Must be used along with the
--basemount-dir parameter. Cannot be used
alongside the --project-dir flag.
-b, --basemount-dir PATH Path to root directory for BaseMount, e.g.
~/basemount/. Must be supplied alongside
--experiment-name parameter.
-o, --out-dir PATH Directory to dump all runs for project.
[required]
-r, --rename Use this flag to automatically re-name the R1
and R2 files to just include the Sample ID.
-v, --verbose Use this flag to enable more verbose output.
--version Use this flag to print the version and exit.
--help Show this message and exit.
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