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[](https://travis-ci.org/johnlees/seer)
# seer
Sequence element enrichment analysis. This document contains
installation instuctions. Usage can be found on the [wiki](https://github.com/johnlees/seer/wiki/Usage), and more information in the [paper](http://www.nature.com/articles/ncomms12797).
## Installation
### Use a pre-compiled release
Head to the [release](https://github.com/johnlees/seer/releases) 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).
### Use on a virtual machine
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](https://www.virtualbox.org/).
### Compile source code
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 <a href="#installation-on-ubuntubiolinux">below</a>
## Dependencies
seer currently depends on
- gzstream <http://www.cs.unc.edu/Research/compgeom/gzstream/>
- armadillo <http://arma.sourceforge.net/>
- boost <http://www.boost.org/>
- dlib <http://www.dlib.net/>
- HDF5 <https://www.hdfgroup.org/HDF5/>
You will also require
- gcc >4.9 or equivalent
- gcc libstdc++ >4.9
You probably already have boost, HDF5 and dlib (as long as you did clone --recursive).
### Installation on Ubuntu/biolinux
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"
### General installation instructions
**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
## Usage, interpretation of results, and troubleshooting
See the [wiki](https://github.com/johnlees/seer/wiki/Usage)
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