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MOSHPIT

MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking

This page contains installation instructions for the MOSHPIT project - this is still work in progress!

Components

The figure below illustrates actions available (green) and being under development (grey).

You can find more information about the individual components in the respective repositories:

Plugin	Source
q2-assembly	https://github.com/bokulich-lab/q2-assembly
q2-moshpit	https://github.com/bokulich-lab/q2-moshpit
q2-checkm	https://github.com/bokulich-lab/q2-checkm

Installation

Before you proceed, make sure you have mamba available in your base environment. Then, to install all the required components, execute:

mamba create -yn q2-shotgun \
    -c conda-forge -c bioconda -c https://packages.qiime2.org/qiime2/2023.5/tested -c defaults \
    q2cli q2-assembly q2-moshpit q2-checkm

There is an issue with QUAST which requires a (hopefully) temporary fix:

conda run -n q2-shotgun \
    pip install --no-deps --force-reinstall git+https://github.com/misialq/quast.git@issue-230

This will create the q2-shotgun QIIME 2 environment, which you can then activate by:

conda activate q2-shotgun

Once active, refresh cache (once) and see which plugins are available:

qiime dev refresh-cache
qiime info

Issues

If you encounter any issues or if there is any feedback you would like to provide, please use the issue tracker in the repository of the respective plugin (see table above). Thanks!