Manual setup

❗Please refer to main README installation one-liner or the detailed setup guide for recommended installation❗

You can manually set up the environments with the following chunks of code.

metaGEM

Conda can take ages to solve environment dependencies when installing many tools at once, we can use mamba instead for faster installation:

# Clone metaGEM repo
git clone https://github.com/franciscozorrilla/metaGEM.git

# Move into metaGEM folder
cd metaGEM

# Create mamba env for faster installation
conda create -n mamba

# Activate mamba env
source activate mamba

# Installl mamba in env
conda install -c conda-forge mamba

# Preferred method for creating metaGEM env using recipe .yml file
mamba env create --prefix ./envs/metagem -f envs/metaGEM_env.yml

# Alternatively metaGEM env setup, note that the line below is commented out
#mamba install python "snakemake>=5.10.0,<5.31.1" fastp megahit bwa samtools=1.9 kallisto concoct=1.1 metabat2 maxbin2 gtdbtk eukrep eukcc smeg motus

# Deactivate mamba env and activate metaGEM env
source deactivate && source activate envs/metagem

# Install pip tools
pip install --user memote carveme smetana

metaWRAP

It is best to set up metaWRAP in its own isolated environment to prevent version conflicts with metaGEM. Note that metaWRAP v1.3.2 has not migrated from python 2 to python 3 yet.

conda create -n metawrap
source activate metawrap
conda install -c ursky metawrap-mg=1.3.2

Or using the conda recipe file:

env create --prefix ./envs/metawrap -f envs/metaWRAP_env.yml

prokka-roary

These bonus pangenome analysis tools caused version conflicts with the core tools in the metagem environment

conda create -n prokkaroary
source activate prokkaroary
conda install prokka roary

Or using the conda recipe file:

env create --prefix ./envs/prokkaroary -f envs/prokkaroary_env.yml

Note that you will still have to install the three dependencies described in the quickstart guide.