---
# System prepended metadata

title: MetaboDirect traning session (Fall 2021)

---

# MetaboDirect traning session (Fall 2021)


## User Manual

MetaboDirect user manual can be accesed [here](https://metabodirect.readthedocs.io/en/latest/index.html#).

## Setting up

### 1. Install Anaconda

Download and install the Anaconda distribution of Python from [here](https://www.anaconda.com/products/individual-b).

### 2. Setting up the command prompt

**(For Windows Users)** Open the *Anaconda Prompt* in Administrator Mode, and enter the following commands:

```
conda install m2-base
conda install -c menpo wget
```

**(Mac Users)** Open your defaul terminal.`ls` and `wget` should already be installed by default,  but to confirm please try:

```
which ls
```
and
```
which wget
```

If you get an error message for any of those, please enter the commands specified above for **Windows users**.

### 3. Python package installation

Install the required packages specified in the **MetaboDirect** [installation page](https://metabodirect.readthedocs.io/en/latest/installation.html):

```
pip install <package-name>
```
### 4. MetaboDirect Installation 

To install MetaboDirect use:

```
pip install metabodirect
``` 

To install the latest version you can use

```
pip install --upgrade metabodirect
```

You can check metabodirect version using

```
metabodirect -v
```

Current version 0.2.5 (as of 9/16/2021)

### 5. Example using test data

Go to your Desktop, for most systems the tilde `~` is your Home directory, the Desktop directory is usually on your home directory. TO quickly got o the Desktop you can type

```
cd ~
cd Desktop
```

Create a new directory

```
mkdir metabodirect_training
```

move in to that directory

```
cd metabodirect_training
```

Example data can be downloaded from the MetaboDirect repository, using the following command:

Report file:

```
wget https://raw.githubusercontent.com/Coayala/MetaboDirect/main/example/Report.csv --no-check-certificate
```

or

```
curl https://raw.githubusercontent.com/Coayala/MetaboDirect/main/example/Report.csv -o Report.csv
```

metadata file:

```
wget https://raw.githubusercontent.com/Coayala/MetaboDirect/main/example/metadata.csv --no-check-certificate
```
or

```
curl https://raw.githubusercontent.com/Coayala/MetaboDirect/main/example/metadata.csv -o metadata.csv
```

### 5.1 Check normalization methods

Use the command

```
test_normalization Report.csv metadata.csv Habitat
```

### 5.2 Run Metabodirect

You can test the example data using

```
metabodirect Report.csv metadata.csv -o test_run -g Habitat -f Sampletype solid -n mean -t
```

Once the transformation files are finished networks can be created using:

```
create_networks test_run metadata.csv Habitat
```


## QUESTIONS

