Xertes0 / msc-bioinformatyka-2022

Motorola Science Cup 2022 - Bioinformatyka

MSC Bioinformatyka 2022

Table of Contents

• About
• Application features
• GitHub pages
• Building from source
• Building the documentation
• Running the tests

About

This application is made for Motorola's science cup.

Application features

• Translates DNA/RNA sequences to protein sequences.
• Highlights and analyzes peptides.
• Draws a skeletal formula of a peptide.
• Displays various information about peptides.

GitHub pages

This project is publicly accessible on GitHub pages under this url.

Building from source

Prerequisites

These are the dependencies required to build this project.

Shared dependencies

These are common dependencies required to build the project.

• git
• CMake
• Ninja or make
• Conan version < 2.0, can be installed using pip

Web dependencies

These are the dependencies required to build and deploy this project on a web server.

• emsdk version 3.1.27
• Yarn

Testing dependencies

These are the dependencies required only to build the c++ library for unit testing.

• C++ compiler (only one)
  • g++ >= 12
  • clang++ >= 16
• ctest (not required but recommended)

Optional dependencies

These dependencies are optional.

• Doxygen For building the documentation as html and man pages

Building the web application

Build the c++ library using emscripten.

# Source the `emsdk`.
source <emsdk_installation_path>/emsdk_env.sh

# Clone and cd into the repository
git clone https://www.github.com/Xertes0/msc-bioinformatyka-2022 && cd msc-bioinformatyka-2022

# Create the build directory and configure CMake
mkdir build-emsdk && cd build-emsdk
emcmake cmake -DCMAKE_BUILD_TYPE:STRING="Release" -DDOXYGEN_ENABLED:BOOL=OFF -DTESTS_ENABLED:BOOL=OFF ..

# Build the project
cmake --build . --parallel $(($(nproc)+1))

Build the web application and generate static HTML pages.

# cd into web directory.
cd <project_dir>/web

# Install dependencies using `yarn`
yarn

# Build static HTML pages.
yarn build

Static html pages will be put in <project_dir>/web/dist which can be now served on a web server. In case you want to run this application on your own web server remember to copy the dist onto the webserver and rename it to msc-bioinformatyka-2022 so the url looks like this: <address>/msc-bioinformatyka-2022/index.html. If you want to change this, modify the vite configuration file <project_dir>/web/vite.config.ts.

Building for unit tests

Build the c++ library and test suite for your system.

# Clone and cd into the repository
git clone https://www.github.com/Xertes0/msc-bioinformatyka-2022 && cd msc-bioinformatyka-2022

# Create the build directory and configure CMake
mkdir build-native && cd build-native
emcmake cmake -DCMAKE_BUILD_TYPE:STRING="Release" -DDOXYGEN_ENABLED:BOOL=OFF -DTESTS_ENABLED:BOOL=ON ..

# Build the project
cmake --build . --parallel $(($(nproc)+1))

How to run the tests

Building the documentation

You can optionally build the documentation as html and man pages with Doxygen. For this use any of the two previous build methods but change the -DDOXYGEN_ENABLED:BOOL=OFF variable to ON when configuring CMake. Then run:

# Build the doxygen documentation
cmake --build . --parallel $(($(nproc)+1)) --target docs

Documentation will be put in <build_dir>/docs/html for static html pages and <build_dir>/docs/man for man pages.

Running the tests

After building the project for unit tests run these commands.

# cd into the build directory
cd <project_dir>/build-native

# Run the tests with ctest (recommended)
ctest

# Or run the tests through the catch2 binary
./tests/tests