ReadServer

Using reference-free compressed data structures to analyse thousands of human genomes simultaneously

For more details, please see our manuscript.

The datasets produced by the analysis in the manuscript are available: ftp://ftp-mouse.sanger.ac.uk/other/tk2/1607-popBWT-material/

Before you start

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This project includes most of its requirements as git submodules. However, many of the modules, as well as the main project itself, require a C++11 compatible compiler (GCC versions from 4.8.1 onwards should work). The following table contains a (non-exhaustive) list of Unix/Linux distributions and the version from which onwards they (should) have a compatible GCC version:

Distribution	Version	Release date (YYYY-MM-DD)	GCC
Fedora	19	2013-07-02	4.8.1
Ubuntu	13.10	2013-10-17	4.8.1
openSUSE	13.1	2013-11-19	4.8.1
Mint	16	2013-11-30	4.8.1
Debian	8.0	2015-04-26	4.9.2
Red Hat Enterprise Linux	RHEL-7.2	2015-11-19	4.8.5
CentOS	7-1511	2015-12-14	4.8.5
Scientific Linux	7.2	2016-02-05	4.8.5
FreeBSD	10.3	2016-04-04	4.8.4

If you install this software on a system that has an incompatible version set as default compiler, make sure to set the CC and CXX shell variables to the location of the binaries of a C++11 compatible compiler and export them in your shell:

export CC='/usr/local/gcc_4_9/bin/gcc-4.9.1'
export CXX='/usr/local/gcc_4_9/bin/g++-4.9.1'

You might also have to add the path to the corresponding 'lib' directories to your LIBRARY_PATH and LD_LIBRARY_PATH variables:

export LD_LIBRARY_PATH='/usr/local/gcc_4_9/lib:/usr/local/gcc_4_9/lib64':$LD_LIBRARY_PATH
export LIBRARY_PATH='/usr/local/gcc_4_9/lib:/usr/local/gcc_4_9/lib64':$LIBRARY_PATH

NOTE:
In case you are planning to compile and run the project in a HPC/Farm/Cluster environment, make sure that you compile on a system with the minimum consensus resource set that is available on ALL nodes in your computing environment! Some components in this project (e.g. 'RocksDB') optimise themselves for the hardware found on the machine they are compiled on. For instance, if the compiling system has SSE 4.2 instruction set the final project will only run on machines with that instruction set.

We tested installation & compilation on a freshly set up Ubuntu 16.04 LTS operating system and found the following required packages not to be included in the standard installation:

• cmake
• automake
• libtool
• texi2html
• texinfo
• docbook2x
• zlib1g-dev
• libbz2-dev
• pkg-config
• unzip

On an Ubuntu system (or any other distribution using the apt package manager and compatible repositories) you can install them with:

sudo apt install cmake automake libtool texi2html texinfo docbook2x zlib1g-dev libbz2-dev pkg-config unzip

(if you don't have administrator rights on your system please ask your IT for help)

Installation

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You can get a clone of this repository by typing

git clone https://github.com/wtsi-svi/ReadServer

or

git clone git@github.com:wtsi-svi/ReadServer.git

in your commandline.

After you have cloned this project, change to the git project directory (e.g. '/usr/local/ReadServer') and execute:

bash install_dependencies.sh

The script should automatically fetch all required submodules and compile them. Afterwards run:

make clean
make
make install

Should you encounter compilation errors when running 'make', add

CC=<path_to_c++11_compatible_c_compiler_binary> CXX=<path_to_c++11_compatible_c++_compiler_binary>

to the 'make' command, e.g.

make CC='/usr/local/gcc_4_9/bin/gcc-4.9.1' CXX='/usr/local/gcc_4_9/bin/g++-4.9.1'

(the paths should be identical to those set for the shell variables).

Once installation is finished, change to the 'demo' sub directory and follow the instructions in 'README.md' to build a demonstration population BWT ReadServer.