Sequence element enrichment analysis. This document contains installation instuctions. Usage can be found on the wiki, and more information in the paper.

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

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).

###Brief 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 reccommend 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

See the wiki