ncbi_datasets_util

This file will become your README and also the index of your documentation.

Developer Guide

If you are new to using nbdev here are some useful pointers to get you started.

Install ncbi_datasets_util in Development mode

# make sure ncbi_datasets_util package is installed in development mode
$ pip install -e .

# make changes under nbs/ directory
# ...

# compile to have changes apply to ncbi_datasets_util
$ nbdev_prepare

Usage

Installation

Install latest from the GitHub repository:

$ pip install git+https://github.com/$GIT_USER_NAME/ncbi_datasets_util.git

or from conda

$ conda install -c $GIT_USER_NAME ncbi_datasets_util

or from pypi

$ pip install ncbi_datasets_util

If ncbi-datasets-cli does not run properly, install from conda

$ conda install bioconda:ncbi-datasets-cli

Documentation

Documentation can be found hosted on this GitHub repository’s pages. Additionally you can find package manager specific guidelines on conda and pypi respectively.

How to use

Fill me in please! Don’t forget code examples:

Usage

To download all genome data for a specific taxon

!ncbi_download -h

!ncbi_qc_summary -h

!ncbi_download_and_qc -h

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