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