Initial Installation for Beginners
These instructions will help novice programmers install all necessary packages and programs needed to run a python program. Mac/Linux OS preferred, these steps outline installation via Anaconda. Other installations should be supported but have had limited testing.
If you are a more advanced programmer, skip to the Installation of AIMS & Required Packages section
Install Anaconda (https://www.anaconda.com/products/individual) to manage the python packages we’re going to be using. This can be a fairly large package, so if space is at a premium for your computer, you can instead install miniconda (https://docs.conda.io/en/latest/miniconda.html). NOTE: Windows users should likely install the full Anaconda package, for a contained environment to run python programs from.
Test that your conda install is working properly by creating a conda environment. Windows OS users, you will likely do this within the Anaconda application. Mac/Linux users, open the terminal application. Once terminal is open, type:
conda create -n aims-env python=3.7
If anaconda/miniconda is installed properly, a Y/N prompt should appear. Type “y” then hit the “enter key” and you will create a conda environment.
If you haven’t already, you should download the code from https://github.com/ctboughter/AIMS.
Next, navigate to the new folder created from this repository. First, open up terminal and enter the environment created earlier by typing:
conda activate aims-env
Windows users will have to activate the environment from within Anaconda
You should now see a little extra bit of text on your terminal command line that looks something like “(aims-env)”. If this didn’t work for some reason, an error message should pop up, otherwise assume you’re fine.
Use terminal to navigate into the newly downloaded folder. If you’ve never used terminal before, you can type in “cd” and then drag and drop the folder into the terminal. Doing so should automatically populate the “path” to the folder. Then hit enter.
When I do this, my terminal line reads:
Hopefully you see something similar (replacing my user name with your own), and when you hit enter you can move to the next step.
Installation of AIMS & Required Packages
The above section focused on the installation of the necessary software to run python programming, as well as basic navigational instructions. In this section, instructions for installing requisite packages and running the GUI Are discussed.
From within the AIMS master directory, type in the terminal:
If you want to use Python 3.9, do not run the above command or install packages in the code block below. Instead, see closed issue #1 on the GitHub page [https://github.com/ctboughter/AIMS/issues/1] for working package versions.
This bash script should run after typing in this command, and you’ll be prompted with a bunch of [y]/n prompts, for which you should consistently enter “y” then the “enter key”.
For more advanced users, you shouldn’t need to use these EXACT package versions, save for Biophython and SciKit-Learn. However, using these versions should guarantee proper functionality of AIMS
If the install_packages.sh script doesn’t work, and you get some kind of an error instead of the prompts, type each of these lines (or copy/paste) one by one, hitting enter after each one:
conda install -c conda-forge biopython=1.76 conda install -c conda-forge scipy=1.4.1 conda install pandas=1.0.3 conda install numpy=1.18.1 conda install matplotlib=3.1.3 conda install scikit-learn=0.22.1 conda install seaborn=0.10.1 conda install -c conda-forge kivy=2.0.0
Everything should now be installed, you should now be able to open up the software! Navigate to the app in terminal by typing:
Launch the GUI with:
From there, the GUI should open. A step by step instruction guide for GUI usage can be found in the AIMS GUI Walkthrough section. If you don’t want to be bothered reading instructions, the app should prevent most major errors. If a “next” button is grayed out, make sure you’ve pressed all of the analysis buttons on the bottom of the current AIMS app screen.
If you’re a more advanced user and would prefer a more customizable experience, check out the AIMS Jupyter Notebooks section.
Lastly, if you’re generally interested in an overview of what AIMS does and how it works, refer to the AIMS Basics.