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/. There are also some Darwin/MacOS specific installation instructions.
I have written these instructions to install STEME into a virtual Python environment using the virtualenv tool. This has the benefits of isolating the STEME install from the rest of your system and can be done without administrator privileges.
The following software should be downloaded and unpacked/installed somewhere on your system:
GCC: I have tested STEME with g++ versions 4.5.1 and 4.6.3 but other recent versions should work. I have had reports that gcc 4.2.1 works on a Mac but that gcc 4.0.1 does not. 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.
sudo apt-get install python-dev python-virtualenv
STEME requires the following Python packages:
Recent versions of weblogolib contain the corebio package which has been removed from PyPI so you probably won’t need to install corebio separately. We will install some of these packages into the operating system as they are fairly standard and widely used. In fact you may well have them installed already:
sudo apt-get install python-numpy python-matplotlib python-biopython
Now create a virtual environment to install STEME into and update PATH so it is used:
mkdir -p $HOME/local virtualenv --system-site-packages $HOME/local/steme-virtualenv export PATH=$HOME/local/steme-virtualenv/bin:$PATH
Now install the other requirements into the virtual environment. You will not need to install corebio if you use a recent version of weblogo:
pip install corebio pip install weblogo pip install cookbook pip install jinja2
The jinja2 package is not absolutely required but with it STEME will produce easy to read HTML output.
Boost C++ libraries: I have tested STEME using version 1.47, 1.48 and 1.49 of boost, although any recent version should work. If you do not already have the libraries installed, first download them:
mkdir -p $HOME/local/src cd $HOME/local/src wget \ http://sourceforge.net/projects/boost/files/boost/1.49.0/boost_1_49_0.tar.bz2/download \ -O boost_1_49_0.tar.bz2 tar jxf boost_1_49_0.tar.bz2
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 $HOME/local/src/boost_1_49_0 ./bootstrap.sh --help ./bootstrap.sh --prefix=$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 STEME uses. I have used the latest SVN version (r12013) of SeqAn, although any recent version should work. You will need subversion to retrieve it and might need cmake to install it:
sudo apt-get install subversion cd $HOME/local/src svn co http://svn.mi.fu-berlin.de/seqan/trunk/seqan cd seqan python util/bin/build_forwards.py core/include/seqan python util/bin/build_forwards.py extras/include/seqan
FFTW3: A library for computing discrete Fourier transforms. Install it:
sudo apt-get install libfftw3-dev
If you do not already have FFTW3 installed and are not running Ubuntu or you do not have administrative privileges you can install FFTW3 from source:
cd $HOME/local/src wget ftp://ftp.fftw.org/pub/fftw/fftw-3.3.2.tar.gz tar zxf fftw-3.3.2.tar.gz cd fftw-3.3.2 CFLAGS=-fPIC ./configure --prefix=$HOME/local make make install
If you have not already done so, download STEME and unpack it locally. You will need to replace *.*.* with the version of STEME you want to install (check at PyPI):
cd $HOME/local/src wget http://pypi.python.org/packages/source/S/STEME/STEME-*.*.*.tar.gz tar zxf STEME-*.*.*.tar.gz cd $HOME/local/src/STEME-*.*.*
We are ready to configure STEME. STEME uses aksetup for installation, which means that installation should be easy and quick. Try:
python configure.py --help
to examine the possible options. By the way, if a configuration option says several ok, then you may specify several values, separated by commas. We need to tell STEME where the boost and seqan C++ libraries are:
python configure.py \ --seqan-dir=$HOME/local/src/seqan/ \ --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 STEME:
python setup.py install
This can take some time to compile. When it has finished, check that STEME has been successfully installed:
You should see a list of STEME’s runtime options.
I have installed STEME successfully on MacOS 10.6.8 using Darwin gcc 4.2.1. Here are some notes that might help you if you run into any problems.
On my MacOS I do not have wget, you should replace it in the above instructions with curl -O. This may not work for the boost download link which you can download manually.
The environment variable LD_LIBRARY_PATH is called DYLD_LIBRARY_PATH on the Mac so this must be changed in the above.
When installing packages using pip, you may see errors such as:
IndentationError: unindent does not match any outer indentation level
You need to edit the file mentioned and remove any blank lines at the end.
If you see errors related to freetype font header files when installing matplotlib, you might be able to work around them with:
# see: http://superuser.com/questions/242190/how-to-install-matplotlib-on-os-x export LDFLAGS="-L/usr/X11/lib" export CFLAGS="-I/usr/X11/include -I/usr/X11/include/freetype2 -I/usr/X11/include/libpng12"
You may need to add -arch i386 -arch ppc -arch x86_64 to CFLAGS when compiling boost and FFTW3.