Metadata-Version: 2.1
Name: BaseMountRetrieve
Version: 0.7.5
Summary: Internal BFSSI package for retrieving files from BaseMount
Home-page: https://github.com/bfssi-forest-dussault/BaseMountRetrieve
Author: Forest Dussault
Author-email: forest.dussault@canada.ca
License: UNKNOWN
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](https://basemount.basespace.illumina.com/) (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 an entire Project (or single Run) 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.
        ```
Platform: UNKNOWN
Description-Content-Type: text/markdown
