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https://github.com/johnlees/seer
sequence element (kmer) enrichment analysis
https://github.com/johnlees/seer
bacteria gwas k-mer
Last synced: about 1 month ago
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sequence element (kmer) enrichment analysis
- Host: GitHub
- URL: https://github.com/johnlees/seer
- Owner: johnlees
- License: gpl-2.0
- Created: 2015-03-01T12:53:07.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2022-11-07T11:20:26.000Z (about 2 years ago)
- Last Synced: 2024-08-02T11:20:00.677Z (4 months ago)
- Topics: bacteria, gwas, k-mer
- Language: C++
- Homepage:
- Size: 1.32 MB
- Stars: 42
- Watchers: 7
- Forks: 9
- Open Issues: 14
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-bacteria - SEER - [C++] - Sequence element (kmer) enrichment analysis. (Software packages / GWAS)
README
[](https://travis-ci.org/johnlees/seer)
[](https://anaconda.org/bioconda/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).
**NOTE:** seer has now been superseded by [pyseer](https://pyseer.readthedocs.io). We would recommend you use that implementation instead.
## Usage, interpretation of results, and troubleshooting
See the [wiki](https://github.com/johnlees/seer/wiki/Usage)
## Installation
These options are roughly listed in increasing order of difficulty. seer only works on Linux.
### Use bioconda
Simply run:
```
conda install seer
```
If you do not have conda, first install [miniconda](https://conda.io/miniconda.html)
then add the necessary channels:
```
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
```
### Use homebrew
If you have homebrew, the following recipe is available:
```
brew tap tseemann/homebrew-bioinformatics-linux
brew tap homebrew/science
brew install seer
```
### 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 below
## Dependencies
seer currently depends on
- gzstream
- armadillo
- boost
- dlib
- 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 , 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
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 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++
: -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