{"id":13543714,"url":"https://github.com/johnlees/seer","last_synced_at":"2025-08-14T17:38:23.625Z","repository":{"id":28002145,"uuid":"31496444","full_name":"johnlees/seer","owner":"johnlees","description":"sequence element (kmer) enrichment analysis","archived":false,"fork":false,"pushed_at":"2022-11-07T11:20:26.000Z","size":1384,"stargazers_count":43,"open_issues_count":14,"forks_count":10,"subscribers_count":6,"default_branch":"master","last_synced_at":"2025-04-02T13:42:17.251Z","etag":null,"topics":["bacteria","gwas","k-mer"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/johnlees.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-03-01T12:53:07.000Z","updated_at":"2025-02-28T17:08:27.000Z","dependencies_parsed_at":"2022-09-19T06:41:50.623Z","dependency_job_id":null,"html_url":"https://github.com/johnlees/seer","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/johnlees/seer","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/johnlees%2Fseer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/johnlees%2Fseer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/johnlees%2Fseer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/johnlees%2Fseer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/johnlees","download_url":"https://codeload.github.com/johnlees/seer/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/johnlees%2Fseer/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270458920,"owners_count":24587495,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-08-14T02:00:10.309Z","response_time":75,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bacteria","gwas","k-mer"],"created_at":"2024-08-01T11:00:35.487Z","updated_at":"2025-08-14T17:38:23.596Z","avatar_url":"https://github.com/johnlees.png","language":"C++","funding_links":[],"categories":["Software packages"],"sub_categories":["GWAS"],"readme":"[![Build Status](https://travis-ci.org/johnlees/seer.svg?branch=master)](https://travis-ci.org/johnlees/seer)\n[![Anaconda-Server Badge](https://anaconda.org/bioconda/seer/badges/version.svg)](https://anaconda.org/bioconda/seer)\n\n# seer\nSequence element enrichment analysis. This document contains\ninstallation 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).\n\n**NOTE:** seer has now been superseded by [pyseer](https://pyseer.readthedocs.io). We would recommend you use that implementation instead.\n\n## Usage, interpretation of results, and troubleshooting\nSee the [wiki](https://github.com/johnlees/seer/wiki/Usage)\n\n## Installation\nThese options are roughly listed in increasing order of difficulty. seer only works on Linux.\n\n### Use bioconda\n\nSimply run:\n```\nconda install seer\n```\n\nIf you do not have conda, first install [miniconda](https://conda.io/miniconda.html)\nthen add the necessary channels:\n```\nconda config --add channels defaults\nconda config --add channels bioconda\nconda config --add channels conda-forge\n```\n\n### Use homebrew\nIf you have homebrew, the following recipe is available:\n```\nbrew tap tseemann/homebrew-bioinformatics-linux\nbrew tap homebrew/science\nbrew install seer\n```\n### Use a pre-compiled release\n\nHead 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).\n\n### Use on a virtual machine\n\nWe have a virtual machine, containing SEER and other useful bioinformatics programs, which is available at\nftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova\nand can be imported as an appliance in [VirtualBox](https://www.virtualbox.org/).\n\n### Compile source code\n\nFirst clone the repository\n\n    git clone --recursive https://github.com/johnlees/seer\n\nIf you already have dlib:\n\n    git clone https://github.com/johnlees/seer\n\nCurrently tested on Linux only, installation should proceed as\n\n    make\n    make install\n\nFull installation instructions are available \u003ca href=\"#installation-on-ubuntubiolinux\"\u003ebelow\u003c/a\u003e\n\n## Dependencies\nseer currently depends on\n\n- gzstream \u003chttp://www.cs.unc.edu/Research/compgeom/gzstream/\u003e\n- armadillo \u003chttp://arma.sourceforge.net/\u003e\n- boost \u003chttp://www.boost.org/\u003e\n- dlib \u003chttp://www.dlib.net/\u003e\n- HDF5 \u003chttps://www.hdfgroup.org/HDF5/\u003e\n\nYou will also require\n\n- gcc \u003e4.9 or equivalent\n- gcc libstdc++ \u003e4.9\n\nYou probably already have boost, HDF5 and dlib (as long as you did clone --recursive).\n\n### Installation on Ubuntu/biolinux\n\nRunning the following commands will install seer\n\n    sudo add-apt-repository ppa:ubuntu-toolchain-r/test\n    sudo apt-get update\n    sudo apt-get install g++-4.9 libhdf5-dev libopenblas-dev libboost-program-options-dev\n\n    git clone --recursive https://github.com/johnlees/seer\n    cd seer\n\n    wget http://www.cs.unc.edu/Research/compgeom/gzstream/gzstream.tgz\n    tar xzf gzstream.tgz\n    cd gzstream \u0026\u0026make CC=/usr/bin/gcc-4.9\n    cd ..\n\n    wget http://sourceforge.net/projects/arma/files/armadillo-6.700.6.tar.gz\n    tar xzf armadillo-6.700.6.tar.gz\n    cd armadillo-6.700.6\n    CXX=/usr/bin/g++-4.9 cmake .\n    make\n    sudo make install\n    sudo ldconfig /usr/lib64\n    cd ..\n    cd src \u0026\u0026 make CXX=/usr/bin/g++-4.9\n\nIf you are having trouble finding hdf5 (e.g. on Ubuntu 16.04) try\nrunning:\n\n    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\"\n\n### General installation instructions\n\n**gzstream**\n\nDownload and unpack to a folder gzstream in the root of the repository. Change into the directory and type\n\n    make\n\n**HDF5**\n\nBest installed with your distribution's package manager. Otherwise use\na binary from \u003chttps://www.hdfgroup.org/HDF5/release/obtain5.html\u003e, or\nif you wish to compile from source\n\n    gunzip \u003c hdf5-X.Y.Z.tar.gz | tar xf -\n    cd hdf5-X.Y.Z\n    ./configure --prefix=/usr/local/hdf5 \u003cmore configure_flags\u003e\n    make\n    make check\n    make install\n    make check-install\n\n**armadillo**\n\nMake sure HDF5 is installed first.\n\nDownload and unpack. Change into directory and type\n\n    cmake -DARMA_USE_HDF5=1 .\n    make\n    make install\n\n**boost**\n\nBest installed with your distribution's package manager, and you should use the c++11 version if possible.\n\nFor a manual installation, see \u003chttp://www.boost.org/doc/libs/1_57_0/more/getting_started/unix-variants.html\u003e 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:\n\n    using gcc:\n      : std11\n      : g++\n      : \u003ccxxflags\u003e-std=c++11\n\nThen run\n\n    ./bootstrap.sh\n    ./b2 install toolset=gcc-std11\n\n\n**dlib**\n\nIf not installed use the above git clone command to include with the\nrepository. Otherwise unpack header files to $(PREFIX)/include\n\n**installation**\n\nCurrently tested on Linux only, installation should proceed as\n\n    make\n    make install\n\nYou may need to explicitly set the current GCC compiler, which you can\ndo by running\n\n    make CXX=g++-4.9\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjohnlees%2Fseer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjohnlees%2Fseer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjohnlees%2Fseer/lists"}