Installation

These installation instructions are specifically for an Ubuntu Linux system but should work with minor changes on other Linux systems and with some changes on other operating systems (Windows, MacOS, etc..). For other Linux systems you will need to replace any invocations of apt-get with your system’s package manager. For other operating systems you will need to work out the corresponding method of install. The instructions install packages using apt-get where possible, otherwise they are installed in $HOME/local/.

I have written these instructions to install pyseqan into a virtual Python environment using the virtualenv tool. This has the benefits of isolating the pyseqan install from the rest of your system and can be done without administrator privileges.

Prerequisites

The following software should be downloaded and unpacked/installed somewhere on your system:

• GCC: I have tested pyseqan with g++ versions 4.7.3 but other recent versions should work. Every release of g++ seems to give it a stricter interpretation of the C++ standard so perhaps it is not a good idea to try a version too much newer. Other modern compilers such as Microsoft C++ should work but I have not tried them. Please let me know if you try other compilers and run into any issues.

  Make sure you have gcc (with g++) installed:

  sudo apt-get install gcc build-essential

  If gcc is not already installed and you do not have administrator privileges you could install it locally from source.

• Python 2.7: Other versions of python 2 will probably work such as 2.5 or 2.6. Install Python with virtualenv:

  sudo apt-get install python-dev python-virtualenv

  Now create a virtual environment to install pyseqan into and activate it:

  mkdir -p $HOME/local
  virtualenv --system-site-packages $HOME/local/pyseqan-virtualenv
  . $HOME/local/pyseqan-virtualenv/bin/activate

• Boost C++ libraries: I have tested pyseqan using version 1.54 of boost, although any recent version should work. You can install the boost libraries with:

  sudo apt-get install libboost-dev

  If you need a different version or want to install from source, first download them:

  mkdir -p $HOME/local/src
  cd $HOME/local/src
  wget \
    http://sourceforge.net/projects/boost/files/boost/1.54.0/boost_1_54_0.tar.bz2/download \
    -O boost_1_54_0.tar.bz2
  tar jxf boost_1_54_0.tar.bz2

  then install boost following the commands given at the Boost website and update your LD_LIBRARY_PATH environment variable so that the shared objects can be found at runtime:

  cd $HOME/local/src/boost_1_54_0
  ./bootstrap.sh --help
  ./bootstrap.sh --prefix=$HOME/local --with-libraries=python
  ./b2 --ignore-config install release
  export LD_LIBRARY_PATH=$HOME/local/lib:$LD_LIBRARY_PATH

• SeqAn sequence analysis library: The SeqAn C++ library provides the suffix array implementation that pyseqan uses. I have used version 1.4.1 of SeqAn, although any recent version should work. You can install a version using apt-get:

  sudo apt-get install seqan-dev

  or install from source:

  cd $HOME/local/src
  wget http://packages.seqan.de/seqan-library/seqan-library-1.4.1.tar.bz2
  tar jxf seqan-library-1.4.1.tar.bz2

Download pyseqan

If you have not already done so, download pyseqan and unpack it locally. You will need to replace *.*.* with the version of pyseqan you want to install (check at PyPI):

cd $HOME/local/src
wget http://pypi.python.org/packages/source/S/pyseqan/pyseqan-*.*.*.tar.gz
tar zxf pyseqan-*.*.*.tar.gz
cd $HOME/local/src/pyseqan-*.*.*

Configure, build, install

We are ready to configure pyseqan. pyseqan uses aksetup for installation, which means that installation should be easy and quick. Try:

python configure.py --help

to examine the possible options. By the way, if a configuration option says several ok, then you may specify several values, separated by commas. We need to tell pyseqan where the boost and seqan C++ libraries are:

python configure.py \
  --seqan-dir=$HOME/local/src/seqan-library-1.4.1/ \
  --boost-inc-dir=$HOME/local/include \
  --boost-lib-dir=$HOME/local/lib

Configuration is obtained from files in this order:

/etc/aksetup-defaults.py
$HOME/.aksetup-defaults.py
$PACKAGEDIR/siteconf.py

Once you’ve run configure, you can copy options from your siteconf.py file to one of these files, and you won’t ever have to configure them again manually. In fact, you may pass the options --update-user and --update-global to configure, and it will automatically update these files for you. This is particularly handy if you want to perform an unattended or automatic installation via pip or easy_install.

Now install pyseqan:

python setup.py install

This can take some time to compile. When it has finished, check that pyseqan has been successfully installed:

python -c "import seqan"

This should run without problems.