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Building ngs-bits from sources (Linux/MacOS)

Dependencies

ngs-bits depends on the following software to be installed

  • g++ (4.5 or higher)
  • qmake (Qt 5.12 or higher, including xmlpatterns, charts and mysql package)
  • git (to extract the version hash)
  • optional: python and matplotlib (for plot generation in QC tools)

For example, the installation of the dependencies using Ubuntu 20.04 looks like that:

    > sudo apt-get install git make g++ qt5-default libqt5xmlpatterns5-dev libqt5sql5-mysql libqt5sql5-odbc libqt5charts5-dev libqt5svg5-dev python3 python3-matplotlib libbz2-dev liblzma-dev libcurl4 libcurl4-openssl-dev zlib1g-dev

Resolving proxy issues with git

If you are behind a proxy that blocks the standard git port, you see something like this:

> git clone --recursive https://github.com/imgag/ngs-bits.git
Cloning into 'ngs-bits'...
fatal: Unable to look up github.com (port 9418) (Name or service not known)

Then you have to adapt your ~/.gitconfig file like that:

[http]
proxy = http://[user]:[password]@[host]:[port]

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

Executing

Now the executables and all required libraries can be found in the bin folder.

Setting the reference genome

Some of the ngs-bits tools need a reference genome in FASTA format.
You can set the reference genome on the command line, e.g. the -ref parameter of the VcfLeftNormalize tool.

To avoid having to set the reference genome for each call, you can set up a settings file.
Copy the template:

> cp bin/settings.ini.example bin/settings.ini

and then set the reference_genome parameter in the bin/settings.ini file.

Setting up the NGSD (optional)

Some of the tools need the NGSD, a MySQL database that contains for example gene, transcript and exon data.
Installation instructions for the NGSD can be found here.

Building GSvar (optional)

GSvar is a GUI for viewing the variant calls produced by the megSAP pipeline.
Additionally, it offers a user interface to the NGSD (see above).

To build GSvar, execute the following command:

> make build_gui_release

Now you need to configure GSVar.

Running a development server on a (local) machine

Setting up a GSvar server for testing (on Ubuntu)

First you need a unused port on the development server. You can either select a random 5-digit port and check with netstat -lntu if the port is already used. Or you can use the following 1-liner to get a free port from the kernel:

> python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'

Additionally you have to provide a certificate. If you do not have a valid certificate for your machine you can create a self-signed one:

> openssl genrsa -out GSvarServer.key 2048
> openssl req -new -key GSvarServer.key -out GSvarServer.csr
> openssl x509 -signkey GSvarServer.key -in GSvarServer.csr -req -days 365 -out GSvarServer.crt

If you use self-signed certificates IGV and libcurl will not work.(See possible fix below)

Next you have to create a GSvarServer.ini in the binfolder:

> cp bin/GSvarServer.ini.example bin/GSvarServer.ini

And fill in all required settings (like port, NGSD credentials, sample paths, ...). If the server runs on a different machine than the client you have to use the hostname/dns name of the server for server_host.

If you use encrypted passwords you have to add the crypt key to the cppCORE directory (sometimes not working on linux) or directly to the cppCORE.pro file.

Next step is to build the server:

> make build_libs_release build_server_release

And run it:

> ./bin/GSvarServer

Now you can adapt the settings in your client and connect to the server.

Trust self-signed certificates on Ubuntu

For the development and testing purposes it is possible to run a local instance of GSvar Server. However, if you are using self-signed certificates, you will have to make them trusted (otherwise IGV and libcurl will not be able to verify them):

Install CA certificates package:

> sudo apt-get install ca-certificates

Copy your self-signed certificate to this location:

> sudo cp YOUR_CERTIFICATE.crt /usr/local/share/ca-certificates

Update the list of certificate authorities:

> sudo update-ca-certificates