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.html 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

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. Import the module in your script

The mOTUs module is not one of the modules that ship with NGLess, so it must be imported with local import (a plain import "motus" is an error, as it refers to the obsolete mOTUs v1 module that is no longer supported):

ngless "1.6"
local import "motus" version "3.1"

NGLess looks for local modules in a Modules directory in the current directory and in the user-data-directory (which is why it was set to /your/folder/ above).

Step 5. Run NGLess

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