1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 | [![Build Status](https://travis-ci.org/johnlees/seer.svg?branch=master)](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 ###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) |
Commit History @debian/1.1.2-2_bpo8+1
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- gbp-buildpackage did not seem to like mentioning the version :-( Andreas Tille 7 years ago
- Add versioned Depends: libarmadillo-dev (>= 1:6.700.6+dfsg-1~bpo8+1) Andreas Tille 7 years ago
- Rebuild for jessie-backports Andreas Tille 7 years ago
- Use -DARMA_USE_HDF5=1 Andreas Tille (commit: Andreas Tille) 8 years ago
- Upload to unstable Andreas Tille 8 years ago
- Add notice to log if test fails but continue building anyway Andreas Tille 8 years ago
- Upstream added -pthread where necessary Andreas Tille 8 years ago
- Adapt patches Andreas Tille 8 years ago
- New upstream version Andreas Tille 8 years ago
- Merge tag 'upstream/1.1.1' Andreas Tille 8 years ago
- Imported Upstream version 1.1.1 Andreas Tille 8 years ago
- Moved packaging from SVN to Git Andreas Tille 8 years ago
- Re-add debian/ dir Andreas Tille 8 years ago
- Imported Upstream version 1.1.0 Andreas Tille 8 years ago
- Merge tag 'upstream/1.1.0' Andreas Tille 8 years ago
- Suggests: fsm-lite (not yet uploaded due to missing license) Andreas Tille 8 years ago
- Tagged 1.1.0-1 Andreas Tille 8 years ago
- Fix hardening Andreas Tille 8 years ago
- Hardening patch does not really work - no idea why (leave this for a later point in time) Andreas Tille 8 years ago
- UPload to new Andreas Tille 8 years ago
- Manpages and other enhancements Andreas Tille 8 years ago
- Polish packaging Andreas Tille 8 years ago
- Use freshly packaged libgzstream-dev Andreas Tille 8 years ago
- Inject seer Andreas Tille 8 years ago
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