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install_unix.md

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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

For Ubuntu 22.04 use the qtbase5-dev package instead of qt5-default.

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.

GSvar is usually running in client-server mode. Thus, you need to setup the GSvar server as well.

Integration with IGV

For all the questions related to IGV, please see the IGV installation page.