metagenomics_pooling_notebook

A collection of Jupyter notebooks and modules to support the wet lab shotgun pipeline.

Installation

Note that this package is designed to be used with Qiita, and some tests will fail without a Qiita installation.

To install this package, first clone the repository from GitHub:

git clone https://github.com/biocore/metagenomics_pooling_notebook.git

Create a Python3 Conda environment in which to run the package:

conda create --yes -n metapool python='python=3.9' scikit-learn pandas numpy nose pep8 flake8 matplotlib jupyter notebook 'seaborn>=0.7.1' pip openpyxl 'seqtk>=1.4'

Activate the Conda environment:

source activate metapool

Change directory to the downloaded repository folder and install:

cd metagenomics_pooling_notebook
pip install -e '.[all]'

For users of notebook version 7.0.0 or higher, table of contents is already installed and can be activated from the pull-down menus. Notebook 6.5.5 users or lower will need to perform the following two additional steps to install and activate table of contents:

First, install the nbextension plugin:

jupyter contrib nbextension install --sys-prefix --skip-running-check

Second, install the table of contents (TOC) extension

jupyter nbextension enable toc2/main

Test

To run all tests, including those that depend on Qiita, type:

cd metagenomics_pooling_notebook
nosetests

Use

The notebooks themselves contain detailed usage instructions.

Ideally, when using a notebook, you will copy the original and use it for each plate you create with the shotgun pipeline.

Just make sure to activate the right Conda environment before starting the notebook.

Here's a quick example:

cp metagenomics_pooling.ipynb ~/New_project/new_project_pooling.ipynb
cd ~/New_project
source activate metapool
jupyter notebook