Virome workflows - NOMIS and ENSEMBLE projects

• Pipeline for annotating viral sequences based on the IMG/VR3 database
• IMGVR3

Setup

Conda

Conda user guide

# install miniconda3
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod u+x Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh # follow the instructions

Getting the repository including sub-modules

git clone --recurse-submodules git@github.com:hpeter0803/viromes.git

Create the main snakemake environment

# create venv
conda env create -f envs/requirements.yaml -n "snakemake"

Running the Pipeline

Adjust the config/config.yaml file with the appropriate paths

• Do the following:

# Running the Pipeline
snakemake --use-conda --cores 36 --jobs 3 -s workflows/Snakefile -rp    

# (OR)

./config/sbatch.sh  # works only on a SLURM-enabled system

Notes:

• Database downloaded from the IMG/VR3 website
• File unzipped as follows:

  gunzip -c IMGVR_all_proteins.faa.gz > IMGVR_all_proteins.faa