semvec/pypi-packages huggingface dataset:
bdgenomics.mango.pileup 0.0.6a1
bdgenomics.mango.pileup
Keywords: ipython,jupyter,widgets,pileup,genome

# bdgenomics.mango.pileup

bdgenomics.mango.pileup is a Jupyter widget that allows users to view genomic reads, variants and features in a Jupyter notebook or in Jupyter lab version >2.0.
bdgenomics.mango.pileup builds off of [pileup.js](https://github.com/hammerlab/pileup.js).

## Installation

### from pip:

    $ pip install bdgenomics.mango.pileup

#### Enable widgets for Jupyter notebook:

    $ jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup  # can be skipped for notebook version 5.3 and above

#### Install widgets for jupyter lab:

    $ jupyter labextension install bdgenomics.mango.pileup

## Running Examples

    $ First run installation, explained above.
    $ cd examples
    $ jupyter notebook

Or run in Jupyter lab:

    $ jupyter lab

### from Source:

For a development installation (requires npm (version >= 3.8) and node (version >= 4.0)):

    $ git clone https://github.com/bdgenomics/mango
    $ cd mango-pileup
    $ rm -r bdgenomics/mango/pileup/static

Install bdgenomics.mango.pileup:

    $ pip install -e .
    $ jupyter nbextension install --py --symlink --sys-prefix bdgenomics.mango.pileup
    $ jupyter nbextension enable --py --sys-prefix bdgenomics.mango.pileup]

Note for developers: the --symlink argument on Linux or OS X allows one to modify the JavaScript code in-place. This feature is not available with Windows.


To install the JupyterLab extension, install the Package, the Jupyter widgets extension, and the bdgenomics.mango.pileup extension:


    $ pip install -e .
    $ cd bdgenomics/mango/js/
    $ jupyter labextension install @jupyter-widgets/jupyterlab-manager # install the Jupyter widgets extension
    $ jupyter labextension install .


#### Testing:

mango-pileup has a Makefile with a ``test`` command to run tests for python and javascript:

    $ make test
BaseMountRetrieve 0.8.1
Internal BFSSI package for retrieving files from BaseMount

# 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.
```