DOC How to run motus3 with NGLess

docs/sources/index.rst

@@ -201,6 +201,7 @@ Authors
    searchpath
    reproducible
    faq
+   motus3
    nglesspy
    cwl
    advanced

docs/sources/motus3.md

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+# 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.embl.de/install/](https://ngless.embl.de/install/) into a conda environment called `ngless`.
+
+## Step 1. Install NGLess-contrib
+
+```bash
+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
+
+```bash
+./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`).
+
+