Environment Setup

The commands described here were created based on the Ubuntu 22.04 operating system and may need to be adapted for other operating systems.

Installation of Python 3.11 and Pip

To prepare Lambda function packages, it is necessary to have Python 3.11 and the package manager Pip installed on your local machine. To check if Python 3.11 is installed, run the following command in the terminal:

python3.11 --version

If Python 3.11 is not installed, you can install it using the following command:

sudo apt-get install python3.11
python3.11 --version
# Python 3.11.0rc1

ls /usr/bin/python*

To check if Pip is installed, run the following command in the terminal:

pip --version

If Pip is not installed, you can install it using the following command:

sudo apt-get install pip
pip --version
# pip 22.0.2 from /usr/lib/python3/dist-packages/pip (python 3.10)

ClustalW Installation

For the execution of the workflow, it is necessary to have ClustalW installed. ClustalW is a software for multiple sequence alignment of protein sequences. One way to obtain this software is as follows:

sudo apt-get install curl

curl "http://www.clustal.org/download/current/clustalw-2.1-linux-x86_64-libcppstatic.tar.gz" -O

tar -xvzf clustalw-2.1-linux-x86_64-libcppstatic.tar.gz

If you are using the Windows operating system, you can download the ClustalW installer from this link: Download ClustalW for Windows

Execution Modes

The project can be executed in two modes: local and lambda.

• The local mode will execute the entire workflow on the local machine.
• The lambda mode should be used for execution using AWS Lambda functions.

Each execution mode has its own specific instructions and configurations. They are detailed in the files local_setup and aws_setup, respectively.

Denethor

The file denethor explains how the workflow execution monitoring system was implemented and which configuration files are used in the execution of activities. Execution by Denethor assumes that the AWS environment setup steps have already been completed.