Installing PLINK/SEQ

This page explains how to install each of the different parts of PLINK/SEQ. All downloads are available on the downloads page. This page covers three topics:

Most visitors will be interested in the standard installation instructions at the top. This will install a set of command line binaries on your system:

  • pseq is the command line interface to PLINK/SEQ
  • pbrowse (a wrapper script), pbrowse.cgi and mongoose are used by the Exome Browser
  • gcol, tab2vcf and behead are minor command-line utilities that can be helpful while working with PLINK/SEQ projects

Note that this does not install the R package; separate installation instructions for Rplinkseq are below. This is not necessary to use all the options of PSEQ; the structure of the overall PLINK/SEQ package is described here.

Note: As mentioned on the downloads page, PLINK/SEQ is still in active development. While PLINK/SEQ is in beta, please report any installation issues to our Google Group.

Binary installation for Linux/Mac

The PLINK/SEQ Linux and Mac downloads are ZIP archives that contains the binary files above. Just download and extract the appropriate ZIP for your machine:


You can copy the exectutables to your command path (e.g. /usr/local/bin or similar), or run them directly from the installation folder.

You should now be able to start PSEQ by typing pseq help at the command line. You can start the browser by typing: pbrowse /path/to/my/project

Installing the Rplinkseq package

The PLINK/SEQ R package (named Rplinkseq) requires the Protocol Buffers library to be installed. Therefore, before you install Rplinkseq, download and install protobuf2.5.0 if it is not already on your machine. The specific version must currently match 2.5.0, which was used to generate files in the PLINK/SEQ library:

# download the source tarball wget # extract it tar -xzf protobuf-2.5.0.tar.gz # enter the base directory cd protobuf-2.5.0 # configure the build system for your machine # install to /usr autoreconf -i ./configure --prefix=/usr # compile the code make # install it make install

Notice that we specify --prefix=/usr. Protobuf installs to /usr/local by default, although here we change the installation directory to /usr instead. This is because some Linux machines do not include /usr/local/lib in LD_LIBRARY_PATH by default.

The instructions above installs Protobuf system-wide. You may wish to install protobuf to a local directory instead, for example if you do not have root access. In this case, simply change --prefix to a local directory: ./configure --prefix=/path/to/local/protobuf/dir

To install Rplinkseq, download and run (from here on, > indicates the R command prompt):

> install.packages("Rplinkseq-0.08.tar.gz")

If protobuf was installed system-wide, Rplinkseq will find it. If it was installed locally, you must tell Rplinkseq where it is by adding the following slightly convoluted argument: > install.packages("Rplinkseq-0.08.tar.gz", configure.args="--with-protobuf=/path/to/protobuf")

You may notice that the value of configure.args is also used when installing PLINK/SEQ by source. In fact, Rplinkseq-0.08.tar.gz contains the C++ source code of the PLINK/SEQ library, which must be compiled by R when you install the package. For this reason, the installation process will probably take 5-10 minutes.

When installation is finished, you can load Rplinkseq like any R package:

> library(Rplinkseq)

This should produce following output:

  PLINK/SEQ genetics library | v0.08 | 15-March-2012

Compiling from source

PLINK/SEQ is written in C++, and it can be compiled from source on most Mac and Linux systems. There are no external dependencies. All that should be required is to download the source tarball, extract, and type make:

tar -xzvf plinkseq-src-0.10.tgz cd plinkseq-0.10 make

If using a Mac, edit the first line of the Makefile to set SYS equal to MAC (i.e uncomment it).

If compilation is successful, then executables should be built in build/execs/.