q2-fondue-examples

Materials accompanying q2-fondue article.

Setup

To run the notebooks in use_cases we suggest you set up a conda environment as follows:

Install mamba in the base environment:

conda install mamba -n base -c conda-forge

Create and activate a conda environment with the required dependencies:

mamba create -yn fondue-pub \
   -c qiime2 -c conda-forge -c bioconda -c udst -c defaults \
   --file requirements.txt

conda activate fondue-pub

pip install \
    git+https://github.com/bokulich-lab/q2-coordinates.git \
    https://github.com/dib-lab/q2-sourmash/archive/master.zip

Install sra-tools using the script provided in the q2-fondue repository.

curl -sLH 'Accept: application/vnd.github.v3.raw' https://api.github.com/repos/bokulich-lab/q2-fondue/contents/install-sra-tools.sh > install-sra-tools.sh

chmod +x install-sra-tools.sh
bash install-sra-tools.sh

rm install-sra-tools.sh

Ensure sra-tools are configured properly (see original repo for details):

vdb-config -i

In case you need to configure a proxy server, run the following command (this can also be done using the graphical interface described above):

vdb-config --proxy <your proxy URL> --proxy-disable no

Finally, install q2-fondue and refresh the QIIME 2 CLI cache:

pip install git+https://github.com/bokulich-lab/q2-fondue.git@5afa120cc8e017a1af6c1200a06326a2e08cc787

qiime dev refresh-cache

Enable QIIME 2's Jupyter extension:

jupyter serverextension enable --py qiime2 --sys-prefix

Note: Visualisation outputs of the Jupyter notebooks in use_cases/ are best viewed in Jupyter Notebook.

Contact

In case of questions or comments feel free to raise an issue in this repository.

License

This repository is released under a BSD-3-Clause license. See LICENSE for more details.

bokulich-lab/q2-fondue-examples

q2-fondue-examples

Setup

Contact

License