andrewdavidsmith/dnmtools

Tools for analyzing DNA methylation data

DNMTools is a set of tools for analyzing DNA methylation data from high-throughput sequencing experiments, especially whole genome bisulfite sequencing (WGBS), but also reduced representation bisulfite sequencing (RRBS). These tools focus on overcoming the computing challenges imposed by the scale of genome-wide DNA methylation data, which is usually the early parts of data analysis.

Installing release 1.1.0

The documentation for DNMTools can be found here. But if you want to install from source and you are reading this on GitHub or in a source tree you unpacked, then keep reading. And if you are in a terminal, sorry for all the formatting.

Required libraries

• A recent compiler: most users will be building and installing this software with GCC. We require a compiler that fully supports C++11, so we recommend using at least GCC 5.8. There are still many systems that install a very old version of GCC by default, so if you have problems with building this software, that might be the first thing to check.
• The GNU Scientific Library: this has always been required. It can be installed using apt on Linux (Ubuntu, Debian), using brew on macOS, or from source available here.
• The Zlib compression library. Most likely you already have this installed on your system. If not, it can be installed using apt on Linux (Ubuntu, Debian) through the package zlib1g-dev. On macOS, Zlib can be installed with brew.
• The HTSlib library, which can be installed through brew on macOS, through apt on Linux (Ubuntu, Debian), or from source downloadable here.

Configuration

• Download dnmtools-1.1.0.tar.gz.
• Unpack the archive:

$ tar -zxvf dnmtools-1.1.0.tar.gz

• Move into the dnmtools directory and create a build directory:

$ cd dnmtools-1.1.0
$ mkdir build && cd build

• Run the configuration script:

$ ../configure

If you do not want to install DNMTools system-wide, or if you do not have admin privileges, specify a prefix directory:

$ ../configure --prefix=/some/reasonable/place

If you installed HTSlib yourself in some non-standard directory, you must specify the location like this:

$ ../configure CPPFLAGS='-I /path/to/htslib/headers' \
               LDFLAGS='-L/path/to/htslib/lib'

Depending on how you obtained HTSlib, the headers may not be in a directory at the same depth as the library file.

Building and installing the tools

If you are still in the build directory, run make to compile the tools, and then make install to install them:

$ make
$ make install

If your HTSlib (or some other library) is not installed system-wide, then you might need to udpate your library path:

$ export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/path/to/htslib/lib

Testing the program

To test if everything was successful, simply run dnmtools without any arguments and you should see the list of available commands:

$ dnmtools

Using a clone of the repo

Not recommended, but if you want to do it this way, we assume you know what you are doing. We strongly recommend using DNMTools through the latest stable release under the releases section on GitHub. Developers who wish to work on the latest commits, which are unstable, can compile the source using a Makefile left in the root of the source tree. If HTSLib and other libraries are available system-wide, compile by running:

$ make

Usage

Read the documentation for usage of individual tools within DNMTools.

Contacts and bug reports

Andrew D. Smith [email protected]

Guilherme de Sena Brandine [email protected]

Copyright and License Information

Copyright (C) 2022 Andrew D. Smith and Guilherme de Sena Brandine

Authors of DNMTools: Andrew D. Smith and Guilherme de Sena Brandine

Essential contributors: Ben Decato, Meng Zhou, Liz Ji, Terence Li, Jenny Qu, Qiang Song and Fang Fang

This is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.