Internal BFSSI package for retrieving files from BaseMount
Project description
BaseMountRetrieve
Package for retrieving files from BaseMount in the output style of a local MiSeq run.
Output Directory Sample
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
Requirements
- BaseMount (Confirmed supported version: Illumina BaseMount v0.15.96.2154)
- Python 3.6
Installation
pip install basemountretrieve
Usage
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]. [required]
-o, --out_dir PATH Directory to dump all runs for project. [required]
-v, --verbose Specify this flag to enable more verbose output.
--version Specify this flag to print the version and exit.
--help Show this message and exit.
Project details
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