Overview:

Sleipnir is a C++ library enabling efficient analysis, integration, mining, and machine learning over genomic data. This includes a particular focus on microarrays, since they make up the bulk of available data for many organisms, but Sleipnir can also integrate a wide variety of other data types, from pairwise physical interactions to sequence similarity or shared transcription factor binding sites.

Docs:

Main documentation: https://functionlab.github.io/sleipnir-docs/

The Sleipnir wiki and bug reporting system are at: (TBD)

The file README.developer has notes for Sleipnir developers.

Sleipnir also includes the code to compile SEEK (the human coexpression search engine). See the link http://seek.princeton.edu/installation.jsp for information on its installation.

Code:

The latest version of Sleipnir software can be obtained by issuing the following command:

git clone https://github.com/FunctionLab/sleipnir.git

Build:

1. Install g++, cmake

2. Install libraries

   • On Mac:
     • brew install libsvm
     • brew install libomp
     • brew install thrift
     • brew install gsl
     • brew install boost
   • On CentOS Linux:
     • sudo yum install libsvm
     • sudo yum install libgomp
     • sudo yum install thrift-devel
     • sudo yum install gsl
     • sudo yum install boost
   • On Ubuntu Linux:
     • apt-get update
     • apt-get install build-essential
     • apt-get install libsvm-dev
     • apt-get install libomp-dev
     • apt-get install libthrift-dev
     • apt-get install libgsl-dev
     • apt-get install libboost-dev
     • apt-get install libboost-graph-dev
     • apt-get install libboost-regex-dev
     • apt-get install libreadline-dev

3. Clone repository

   • git clone https://github.com/FunctionLab/sleipnir.git
   • cd sleipnir
   • git submodule init
   • git submodule update

4. Prep make files with cmake

   • mkdir Debug
   • cd Debug/
   • cmake -DCMAKE_BUILD_TYPE=Debug ..
   • Alternately replace 'Debug' with 'Release' in all the above commands to make the release build

5. Build the code

   • (On Mac) - Edit sleipnir/src/libsvm.h
     • Replace: #include <libsvm/svm.h>
     • With: #include <svm.h>
   • cd Debug/
   • make
     • In case of errors:
       • make clean
       • make VERBOSE=1

6. [Optional] Install SVM_PERF libraries to build: Data2SVM, SVMperfer, SVMperfing, SVMfe, SVMer

   • wget http://download.joachims.org/svm_perf/current/svm_perf.tar.gz
   • mkdir svm_perf; cd svm_perf; tar xzvf ../svm_perf.tar.gz
   • make
   • ar rcs libsvmperf.a *.o /.o
   • cd ..; cp -a svm_perf /usr/local/lib/
   • ln -s /usr/local/lib/svm_perf/libsvmperf.a /usr/local/lib
   • ln -s /usr/local/lib/svm_perf /usr/local/include

Tests:

0. One-time prep: create the conda environment (by default this will create the 'genomics' conda env)

   • conda env create --file scripts/seek/conda_environment.yml

1. Run the c++ unit tests

   • Debug/tests/unit_tests

2. Test the scripts for building and merging SEEK database compendiums

   • conda activate genomics
   • python -m pytest -s -v scripts/seek/tests

3. Run the SEEK system tests (test SeekMiner and SeekRPC)

   • conda activate genomics
   • python -m pytest -s -v tests/

4. Run Seek DB tests (test that the database gives expected bio-informative results). These tests can only be run where the full SEEK database is installed.

   • cd tests/bioinform_tests
   • PREP: Install and init Git LFS (Large File Storage)
     • On Mac: brew install git-lfs
     • On Centos: yum install git-lfs
     • On Ubuntu: apt-get install git-lfs
     • Initialize git-lfs: git lfs install
     • Refresh the gold standard tgz files (should be multipe MB in size)
       • rm gold_standard_results/*
       • git restore gold_standard_results/*
   • Run the tests: (The bioinform test has an option for different lengths of test, i.e. how many queries are run)
     • bash run_paramtest.sh -v -s <path_to_seek_db> -b <path_to_seek_binaries>
     • bash run_querysize.sh -v -s <path_to_seek_db> -b <path_to_seek_binaries>
     • bash run_bioinform.sh -v -s <path_to_seek_db> -b <path_to_seek_binaries> -t [tiny,short,medium,long]