Quick Start (TLDR;)

Are you a reviewer or just need to test this out quickly? The commands below will allow you to install and test MP-3.5 quickly and efficiently. Sorry you still need Conda/Mamba.

Note

If you run the last two commands, make sure to replace the ${variables} with real values.

Try it with Mamba (recommended)

# install metapathways with Mamba
mamba create -n metapathways_env -c hallamlab -c bioconda -c conda-forge metapathways
mamba activate metapathways_env

# test the install
metapathways build_db --test
metapathways run --test # results in `${CWD}/test`

### Try your own data! ###

# build the minimal reference DB
metapathways build_db -d ${path/to/MPDB} --func swissprot -a fast

# run minimal DB on your personal data
metapathways run -i ${your_metagenome.fa} -o ${path/to/output_dir} -d ${path/to/MPDB}

Note

The build_db test does not create a DB that is to be used for downstream DB builds. For the full reference build the use is to provide a location with acceptable storage capacity and accessibility.

Try it with Docker

# pull down with docker
docker pull quay.io/hallamlab/metapathways
docker run -it quay.io/hallamlab/metapathways /bin/bash

# test the install (within docker)
metapathways build_db --test
metapathways run --test # results in `${CWD}/test`

### Try your own data! ###

# build the minimal reference DB
metapathways build_db -d ${path/to/MPDB} --func swissprot -a fast

# run minimal DB on your personal data
metapathways run -i ${your_metagenome.fa} -o ${path/to/output_dir} -d ${path/to/MPDB}