Requirements and installation

The main requirements are:

• gcc/g++
• git and git lfs
• conda

Most other dependencies are either included as a git submodule or will be installed automatically by snakemake using the conda YAML files in envs/. However, some tools need to be installed and/or configured manually.

Miniconda (conda)

# 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

PathoFact

Clone the repository and its sub-modules:

# activate git lfs
git lfs install
# clone branch incl. sub-modules
git clone -b master --recursive https://git-r3lab.uni.lu/laura.denies/PathoFact.git

Pipeline environment

# create the conda environment
conda env create -f=envs/PathoFact.yaml

You can activate and deactivate the environment using conda activate PathoFact and conda deactivate, respectively.

Dependency: SignalP

Required version: 5.0

To download the tool you need to submit a request at https://services.healthtech.dtu.dk/:

• Look for "SignalP" and click on the link
• Click on "Downloads"
• Click on the link for your platform for the version "Version 5.0g"
• Fill and submit the form

After the installation, adjust the path for this tool in config.yaml (keyword signalp).