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Building ngs-bits from sources MacOS

Dependencies

ngs-bits depends on the following software to be installed

  • XCode
  • qmake (Qt 5.12 or higher, including xmlpatterns and mysql package)
  • git (to extract the version hash)
  • optional: python and matplotlib (for plot generation in QC tools)
  • also optional: home brew (makes easier to install other depdendencies)

This documentation assumes that you install dependencies using Brew. First of all, you are going to need Qt. Since the default version in Brew is currently 6, you need to force it to use version 5 (ngs-bits cannot be compiled with Qt 6):

> brew install qt@5

If you want to develop under MacOS, you need to install Qt Creator IDE:

> brew install qt-creator

Configuring Qt Creator

Having installed Qt Creator, Qt binary location should be specified. Usually it is at /usr/local/Cellar/qt@5/5.15.2_1/bin/qmake (path may vary, depending on the version number)

MySQL Plugin

To enable the database related functionality, a MySQL plugin has to be built. For the most other platforms it is avaliable as a binary package, but not for MacOS. On MacOS you need to get Qt source code and to compile the plugin by your self:

> git clone git://code.qt.io/qt/qt5.git
> git checkout 5.15
> git submodule update --recursive --init

The last step may take a lot of time, since some module are huge. It is recommended to exclude WebEngine modules. Now you need to go the qtbase module and find the plugin:

> cd qtbase/src/plugins/sqldrivers

Compile and install the plugin:

> qmake
> make sub-mysql
> make install

Running the Database Server in a Docker Container

You don't have to install MySQL server on your machine, you can run it in a Docker container instead:

> docker run -d --name my-own-mysql -p 3306:3306 -e MYSQL_ROOT_PASSWORD=mypass123 mysql:5.7
> docker run --name my-own-phpmyadmin -d --link my-own-mysql:db -p 8081:80 phpmyadmin/phpmyadmin

PhpMyAdmin can now be accessed from a browser at (use root as the username and the password from the above):

> https://localhost:8081

Just import your database dump and you are ready to go.

Build

Just execute the following make commands:

> make build_3rdparty
> make build_libs_release
> make build_tools_release

If you need to build a different version of htslib, please follow these instructions

Deployment

For yet unknown reasons, GSvar could not detect *.dylib files located at the same folder on testing machines. It searches for the libraries at /usr/local/lib instead.

Currently used temporary fix looks like that:

> cp libcppXML.1.0.dylib /usr/local/lib/libcppXML.1.dylib
> cp libcppGUI.1.0.dylib /usr/local/lib/libcppGUI.1.dylib
> cp libcppNGS.1.0.dylib /usr/local/lib/libcppNGS.1.dylib
> cp libcppNGSD.1.0.dylib /usr/local/lib/libcppNGSD.1.dylib
> cp libcppVISUAL.1.0.dylib /usr/local/lib/libcppVISUAL.1.dylib
> cp libcppCORE.1.0.dylib /usr/local/lib/libcppCORE.1.dylib

All settings should be saved at /Users/megalex/github/ngs-bits/bin/GSvar.app/Contents/MacOS

Development Environment

GSvar can be build from inside Qt Creator by using its standard mechanisms:

> tools_gui -> Release -> GSvar

Note: The above mentioned processes have been tested on Intel-based Macs. It remains unknown if GSvar can be compiled natively for M1 CPUs (Qt 5 does not officially/completly support M1 chips yet). However, they claim it works through the Rosetta translation layer, native arm64 support seems to be under development. Qt 6 should officially support Apple Silicon.