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Michal Ziemski edited this page May 22, 2023
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MOdular SHotgun metagenome Pipelines with Integrated provenance Tracking
This page contains installation instructions for the MOSHPIT project - this is still work in progress!
| 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 |
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
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
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!