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Installation

Installation via conda

Note (9/26/2023) Although conda currently works, it seems that using mamba is more reliable. If you have conda installed, you can install mamba very easily by following instructions here:

https://anaconda.org/conda-forge/mamba

In the instructions below, replacing conda with mamba should work the same (and, in some cases, more reliably), but with mamba.

Right now conda is probably the easiest way to install dnmtools. Dnmtools is among the bioconda recipes. If you know how to use conda and are setup to use bioconda, then you might simply be able to do:

$ conda install dnmtools

If you have problems with this, then you can try:

$ conda install -c conda-forge -c bioconda --strict-channel-priority dnmtools

The dependencies for dnmtools might themselves have dependencies that are in the conda-forge channel. Using --strict-channel-priority is recommended by bioconda.

  • Conda: you can find installation instructions here.

  • Bioconda: additional helpful setup instructions can be found here.

If you encounter further problems, try creating a new environment for dnmtools within conda:

$ conda create --name dnmtools_env
$ conda activate dnmtools_env
$ conda install -c conda-forge -c bioconda --strict-channel-priority dnmtools

Above, you would have a new environment called dnmtools_env that would need to be activated when you want to use dnmtools.

Building dnmtools from source release

Required libraries

  • A recent compiler. Most users will be building and installing this software with GCC. We require a compiler that fully supports C++17, so we recommend using at least GCC 9 (released in 2019). 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 clang LLVM compiler can also be used with a recent enough version.
  • The GNU Scientific Library. It can be installed using apt on Linux (Ubuntu, Debian), using brew on macOS, or from source available here.
  • The HTSlib library. This can be installed through brew on macOS, through apt on Linux (Ubuntu, Debian), or from source downloadable 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.

Configuration

$ tar -zxvf dnmtools-1.5.1.tar.gz
  • Move into the dnmtools directory and create a build directory:
$ cd dnmtools-1.5.1
$ 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

There is a test suite for dnmtools and these test can be performed as follows:

make check

This must be done from the build directory. Note that the tests performed with make check are mostly regression tests that cover prior issues rather than coverage tests to test all the functionality of dnmtools.

Using a clone of the repo

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 start the process using the autogen.sh script and then using the usual autotools approach.