How to integrate mOTUs3 with NGLess

This document describes how to integrate mOTUs3 with NGLess. You will need to replace /your/folder/ with the path to the folder where you want to install mOTUs3.

Step 0. Install NGLess

Install NGLess following the instructions at https://ngless.readthedocs.io/en/latest/install/ into a conda environment called ngless.

Step 1. Install NGLess-contrib

conda activate ngless

git clone https://github.com/ngless-toolkit/ngless-contrib.git
cd ngless-contrib

change the directory in install.sh in line 7 to a folder in (/your/folder/Modules/ in the example, it is very important that the last directory is Modules)

Step 2. Install mOTUs3

Run

./install.sh
cd /your/folder/Modules/motus.ngm/3.1

Run

```bash` python -m venv mOTUs-3.1.0-venv &&
source mOTUs-3.1.0-venv/bin/activate &&
wget https://github.com/motu-tool/mOTUs/archive/3.1.0.tar.gz &&
tar xf 3.1.0.tar.gz &&
rm -f 3.1.0.tar.gz &&
pip install ./mOTUs-3.1.0 &&
motus downloadDB && rm -rf mOTUs-3.1.0

## Step 3. Create an NGLess configuration file


Create an `ngless.conf` file with following lines (saved in `/your/folder/ngless.conf`):

user-directory = “/your/folder/” user-data-directory = “/your/folder/” temporary-directory= “/scratch/your_folder/temp/”

## Step 4. Run NGLess

Run `ngless` with the option `--config-file /your/folder/ngless.conf` (for debugging, run `ngless` with the option `--trace`).