Sequence element enrichment analysis. This document contains installation instuctions. Usage can be found on the wiki, and more information in the paper.
NOTE: seer has now been superseded by pyseer. We would recommend you use that implementation instead.
See the wiki
These options are roughly listed in increasing order of difficulty. seer only works on Linux.
Simply run:
conda install seer
If you do not have conda, first install miniconda then add the necessary channels:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
If you have homebrew, the following recipe is available:
brew tap tseemann/homebrew-bioinformatics-linux
brew tap homebrew/science
brew install seer
Head to the release page and download and unpack the tarball. If you have the dependencies installed use the dynamic version, otherwise use the static version (tested on Ubuntu only; static_all should work on other 64-bit Linux platforms).
We have a virtual machine, containing SEER and other useful bioinformatics programs, which is available at ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova and can be imported as an appliance in VirtualBox.
First clone the repository
git clone --recursive https://github.com/johnlees/seer
If you already have dlib:
git clone https://github.com/johnlees/seer
Currently tested on Linux only, installation should proceed as
make
make install
Full installation instructions are available below
seer currently depends on
You will also require
You probably already have boost, HDF5 and dlib (as long as you did clone --recursive).
Running the following commands will install seer
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install g++-4.9 libhdf5-dev libopenblas-dev libboost-program-options-dev
git clone --recursive https://github.com/johnlees/seer
cd seer
wget http://www.cs.unc.edu/Research/compgeom/gzstream/gzstream.tgz
tar xzf gzstream.tgz
cd gzstream &&make CC=/usr/bin/gcc-4.9
cd ..
wget http://sourceforge.net/projects/arma/files/armadillo-6.700.6.tar.gz
tar xzf armadillo-6.700.6.tar.gz
cd armadillo-6.700.6
CXX=/usr/bin/g++-4.9 cmake .
make
sudo make install
sudo ldconfig /usr/lib64
cd ..
cd src && make CXX=/usr/bin/g++-4.9
If you are having trouble finding hdf5 (e.g. on Ubuntu 16.04) try running:
make CPPFLAGS="-I../gzstream -I../dlib -I/usr/include/hdf5/serial -D DLIB_NO_GUI_SUPPORT=1 -D DLIB_USE_BLAS=1 -D DLIB_USE_LAPACK=1"
gzstream
Download and unpack to a folder gzstream in the root of the repository. Change into the directory and type
make
HDF5
Best installed with your distribution's package manager. Otherwise use a binary from https://www.hdfgroup.org/HDF5/release/obtain5.html, or if you wish to compile from source
gunzip < hdf5-X.Y.Z.tar.gz | tar xf -
cd hdf5-X.Y.Z
./configure --prefix=/usr/local/hdf5 <more configure_flags>
make
make check
make install
make check-install
armadillo
Make sure HDF5 is installed first.
Download and unpack. Change into directory and type
cmake -DARMA_USE_HDF5=1 .
make
make install
boost
Best installed with your distribution's package manager, and you should use the c++11 version if possible.
For a manual installation, see http://www.boost.org/doc/libs/1_57_0/more/getting_started/unix-variants.html for details on how to use ./b2 to install. I recommend that you create a user-config.jam file in the boost root which modifies the gcc compilation:
using gcc:
: std11
: g++
: <cxxflags>-std=c++11
Then run
./bootstrap.sh
./b2 install toolset=gcc-std11
dlib
If not installed use the above git clone command to include with the repository. Otherwise unpack header files to $(PREFIX)/include
installation
Currently tested on Linux only, installation should proceed as
make
make install
You may need to explicitly set the current GCC compiler, which you can do by running
make CXX=g++-4.9