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# Requirements and installation
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The main requirements are:
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- `gcc/g++`
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- `git` and `git lfs`
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- `conda`
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Most other dependencies are either included as a `git submodule` or will be installed automatically by `snakemake` using the `conda` YAML files in `envs/`.
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However, some tools need to be installed and/or configured manually.
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## Miniconda (conda)
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```bash
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# install miniconda3
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wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
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chmod u+x Miniconda3-latest-Linux-x86_64.sh
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./Miniconda3-latest-Linux-x86_64.sh # follow the instructions
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```
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## PathoFact
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Clone the repository and its sub-modules:
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```bash
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# activate git lfs
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git lfs install
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# clone branch incl. sub-modules
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git clone -b master --recursive https://git-r3lab.uni.lu/laura.denies/PathoFact.git
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```
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## Pipeline environment
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```bash
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# create the conda environment
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conda env create -f=envs/PathoFact.yaml
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```
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You can activate and deactivate the environment using `conda activate PathoFact` and `conda deactivate`, respectively.
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## Dependency: `SignalP`
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Required version: `5.0`
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To download the tool you need to submit a request at https://services.healthtech.dtu.dk/:
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- Look for "SignalP" and click on the link
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- Click on "Downloads"
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- Click on the link for your platform for the version "Version 5.0g"
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- Fill and submit the form
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After the installation, adjust the path for this tool in `config.yaml` (keyword `signalp`). |