Installing DEploidIBD

Please note that the following installation instructions were derived from those described in the github repository.

Step 1: Preparing for C++ compilation.

DEploidIBD is implemented in C++ and the code needs to be compiled to your local computer hardware before it can run.

MacOS Use the package manager Homebrew to install autoconf and other tools necessary for compilation:

brew install pkg-config automake autoconf autoconf-archive cppunit

Ubuntu/Debian For Ubuntu or Debian operaing systems, use the package manager apt-get to install the compilation tools:

apt-get install build-essential autoconf autoconf-archive libcppunit-dev zlib1g-dev

Step 2: Clone the repository.

Use git to clone the repository:

git clone https://github.com/DEploid-dev/DEploid.git
cd DEploid
git submodule update --init --recursive --remote

Step 3: Compile!

Finally, you can compile DEploidIBD with the following commands:

./bootstrap
make

If the compilation has run successfully, you should be able to run the DEploidIBD executable with:

./dEploid

The github repository also includes some example data and commands. For example, you can run:

./dEploid \
 -vcf data/testData/PG0390-C.test.vcf \
 -plaf data/testData/labStrains.test.PLAF.txt 
 -o PG0390-CNopanel \
 -noPanel

which will produce a set of example output files.

Recommended: Adding DEploidIBD to your bash PATH If we want to run the dEploid executable from anywhere, we need to add it to our PATH variable in bash. To do this, first make sure you are in the root directory of the DEploidIBD github repository. Then, run:

export PATH=$PATH:`pwd`

Now, you should be able to run dEploid from any folder.

Additional resources: The DEploid manual page There are some additional instructions on how to run DEploid and the meaning of individual flags available in the github repository. First, navigate into the cloned DEploid directory on your local machine, e.g. cd DEploid. Then, run:

man docs/_build/man/dEploid.1

Step 4: Installing other tools required for the tutorial

In the upcoming sections of the tutorial we will make use of a command-line VCF manipulation tool called bcftools. bcftools can be installed in a variety of ways, but I would recommend doing so using conda.

If you have not already, install conda following the appropriate instructions here.

Next, we will create a virtual environment for the tutorial that contains bcftools with the following command:

conda create -n deploid -c bioconda bcftools

For Mac you can also install bcftools by running:

brew install bcftools

Once this is done, you should be able to activate your environment with:

conda activate deploid

Running bcftools should display the help menu which includes a list of available subcommands. We are now ready to proceed with the first part of the tutorial.