Installation

To install the VNTRseek pipeline, download either the binary gzipped file from our download page or download and compile the source archive by following the directions below.

Note: TRF is also required, but is downloaded during installation. If for some reason the download fails, you can download it manually from the TRF homepage and save it as trf409-ngs.linux.exe in the build directory (see below).

Installation requirements can be found under Requirements.

Building from source

Download the source archive from the GitHub releases tab or clone the repository using:

git clone https://github.com/yzhernand/VNTRseek.git

Then build (see below for more options):

tar xzvf vntrseekN.NN.tar.gz
cd vntrseekN.NNsrc
mkdir build
cd build
cmake ..     # may be cmake28 on some systems
make install # or sudo make install, if needed

Note the space and two dots after "cmake".

By default, this will install the pipeline to /usr/local/vntrseekN.NN (eg, /usr/local/vntrseek1.08).

If you would like to choose a different installation prefix, simply run:

cmake -DCMAKE_INSTALL_PREFIX=<full path> ..

For example, to install to your home directory, ${HOME}/vntrseekN.NN, use:

cmake -DCMAKE_INSTALL_PREFIX=${HOME} ..

You can change your default compiler using -DCMAKE_C_COMPILER=yourcompiler. For example, to use clang:

cmake -DCMAKE_C_COMPILER=clang ..

Reference files

To complete the installation, copy three hg19 prepared reference files into the installation folder from the .data.tar.gz file (see downloads page).

To use another genome you will need to prepare data files using TRDB (https://tandem.bu.edu/cgi-bin/trdb/trdb.exe). Also set the MySQL credentials in the global vs.cnf file (optionally they can be set using command line options). CREATE DATABASE privileges must be granted.

If you installed to a non-standard location, you may need to add /path/to/prefix/bin to your PATH variable (eg, if your prefix was /opt, you will need to have /opt/bin in your PATH).

Post install configuration

We do not recommend running VNTRseek as root. Therefore, if VNTRseek was installed using root privileges, or you are running it in an environment where one central installation is used by a team, we suggest that users of the pipeline are all assigned to the same group. Then, change the group ownership of the install directory, and all files/directories within, to that group.