Installation

TODO: MetaboBlend is not yet released on conda/pypi TODO: change package name

Conda (recommended)

Install Miniconda, follow the steps described here

Start the conda prompt

• Windows: Open the Anaconda Prompt via the Start menu

• macOS or Linux: Open a Terminal

Create a metaboblend specific conda environment. This will install a the dependencies required to run metaboblend:

$ conda create --yes --name metaboblend -c conda-forge -c bioconda -c computational-metabolomics

Note

• The installation process will take a few minutes.

• Feel free to use a different name for the Conda environment

You can use the following command to remove a conda environment:

$ conda env remove -y --name metaboblend

This is only required if something has gone wrong in the previous step.

Activate the metaboblend environment:

$ conda activate metaboblend

To test your metaboblend installation, in your Conda Prompt, run the command:

$ metaboblend --help

or:

$ python
import metaboblend

Close and deactivate the metaboblend environment when you’re done:

$ conda deactivate

PyPi

Install the current release of metaboblend with pip:

$ pip install metaboblend

Note

• The installation process will take a few minutes.

To upgrade to a newer release use the --upgrade flag:

$ pip install --upgrade metaboblend

If you do not have permission to install software systemwide, you can install into your user directory using the --user flag:

$ pip install --user metaboblend

Alternatively, you can manually download metaboblend from GitHub or PyPI. To install one of these versions, unpack it and run the following from the top-level source directory using the Terminal:

$ pip install .

Testing

MetaboBlend uses the Python unittest testing package.