q2d2: QIIME 2 is documentation-driven (a public prototype)
This repository is a publicly accessible prototype of some ideas that we're exploring for QIIME 2. This repository is not QIIME 2 - that doesn't exist yet. The code in this repository is untested and highly experimental. You should not use this for any real analysis, only for exploring the documentation-driven interface.
Installation (conda-based)
conda create -n q2d2 python=3.4 scikit-bio 'ipython-notebook<4.0.0' 'ipython<4.0.0'
source activate q2d2
pip install -U --no-deps https://github.com/biocore/scikit-bio/archive/master.zip
git clone https://github.com/gregcaporaso/q2d2.git
cd q2d2
pip install -e .Usage
Run the following commands to generate analysis notebooks:
q2d2 create-study --study-id my-study --sample-metadata-filepath $PWD/example-data/keyboard/sample-md.tsv --otu-metadata-filepath $PWD/example-data/keyboard/q191/otu-md.tsv --tree-filepath $PWD/example-data/keyboard/q191/rep-set.tre --unrarefied-biom-filepath $PWD/example-data/keyboard/q191/otu-table.tsv
ipython notebook my-study/index.md