# MetaboDirect traning session (November 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 ``` 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. R package installation Open R or RStudio and install the required packages specified in the **MetaboDirect** [installation page](https://metabodirect.readthedocs.io/en/latest/installation.html): ``` install.packages('<package-name>') ``` The packages *KEGGREST* needs to be installed from Bioconductor with the following command: ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("KEGGREST") ``` The package *pmartR* needs to be installed with *devtools* with the following command: ``` devtools::install_github("pmartR/pmartR") ``` Please check each package documentation for more detailed information regarding installation. ### 5. Put R in your system's PATH Check i R is in your path by typing the following in the command prompt ``` which Rscript ``` If you get and error, R is not in your path: **(For Windos Users)** Please follow the instructions of this [website](https://www.architectryan.com/2018/03/17/add-to-the-path-on-windows-10/) to add the directory where R is installed to your system's path. **(For Mac Users)** Most likely R will be already in your path. If not, you can follow the instructions of this [website](https://www.architectryan.com/2012/10/02/add-to-the-path-on-mac-os-x-mountain-lion/) ### 6. 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 0.2.7 (as of 11/17/2021) ### 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: ``` curl https://raw.githubusercontent.com/Coayala/MetaboDirect/main/example/Report.csv -o Report.csv ``` metadata file: ``` 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