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searchpath | ||
reproducible | ||
faq | ||
motus3 | ||
nglesspy | ||
cwl | ||
advanced | ||
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# How to integrate mOTUs3 with NGLess | ||
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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. | ||
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## Step 0. Install NGLess | ||
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Install NGLess following the instructions at [https://ngless.embl.de/install/](https://ngless.embl.de/install/) into a conda environment called `ngless`. | ||
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## Step 1. Install NGLess-contrib | ||
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```bash | ||
conda activate ngless | ||
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git clone https://github.com/ngless-toolkit/ngless-contrib.git | ||
cd ngless-contrib | ||
``` | ||
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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`) | ||
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## Step 2. Install mOTUs3 | ||
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Run | ||
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```bash | ||
./install.sh | ||
cd /your/folder/Modules/motus.ngm/3.1 | ||
``` | ||
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Run | ||
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```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`). | ||