AMiGA Anaylsis of Microbial Growth Assays

• Home
• Documentation
• Configuration
• Get Time at Threshold
• Estimate Confidence
• Code Vignette
• Compare Parameters
• Normalize Parameters
• Pool Replicates
• Detect Diauxie
• Command Line Interface
• Plot Heatmaps
• Test Hypotheses
• Subset Data
• Batch Analyze
• Fit Curves
• Summarize & Plot
• Prepare Metadata
• Prepare Data
• Install AMiGA
• Example Pipeline

Table of Contents

• Overview
• Instructions for Advanced Users
• Instructions for Beginners
  • Installing AMiGA with pip
  • Installing AMiGA with conda/mamba

Overview

AMiGA is available on PyPI and Bioconda and is compatible with Python versions 3.10, 3.11, and 3.12.

Note to Windows users: If you would like to install AMiGA with conda/mamba, you will need to use the Windows Subsystem for Linux, becuase AMiGA is only available through the bioconda channel for linux and mac systems.

Note to all users: To avoid dependency conflicts, I recommend that you create a virtual environment for AMiGA.

• For pip users, see Install packages in a virtual environment using pip and ven.
• For conda/mamba users, see Managing environments.

Instructions for Advanced Users

AMiGA can be installed by pip or conda/mamba and is compatible with Python 3.10, 3.11, and 3.12. I recommend that you create a virtual environment for AMiGA.

pip install amiga

conda install bioconda::amiga

mamba install bioconda::amiga

If you would like to build AMiGA locally, then do the following.

git clone https://github.com/firasmidani/amiga
cd amiga
python3 -m install build
python3 -m build .
python3 -m pip install dist/amiga*whl

You can test your installation by pulling up the help menu.

amiga -v              # display AMiGA version numbers
amiga -h              # help menu
amiga summarize -h    # help menu for summarize command

Instructions for Beginners

These are instructions for beginners who have never used python packages or need a referesher on how to install and run python packages.

Installing AMiGA with pip

I recommend that you install AMiGA with pip if you use Windows and do not want to install Windows Subsystems for Linux. See detailed instructions here.

Installing AMiGA with conda/mamba

Otherwise, I recommend that you install AMiGA with conda or mamba. See detailed instructions here.