mkdir build
  cd build
  cmake ..
  make

  brew tap homebrew/versions
  brew tap homebrew/science
  brew install gcc5 cmake R

  export CXX=g++-5
  export CC=gcc-5
  export LDFLAGS="-static-libgcc -static-libstdc++"

  mkdir build
  cd build
  cmake ..
  make

  BaMMmotif DIRPATH FILEPATH [OPTIONS]

  Bayesian Markov Model motif discovery software.

  DIRPATH
      Output directory for the results.

  FILEPATH
      FASTA file with positive sequences of equal length.

  --negSequenceSet <FILEPATH>
      FASTA file with negative/background sequences used to learn the
      (homogeneous) background BaMM. If not specified, the background BaMM
      is learned from the positive sequences.

  --reverseComp
      Search motifs on both strands (positive sequences and reverse
      complements). This option is e.g. recommended when using sequences
      derived from ChIP-seq experiments.

  --bindingSiteFile <FILEPATH>
      File with binding sites of equal length (one per line).

  --markovModelFile <FILEPATH>
      File with BaMM probabilities as obtained from BaMM!motif (omit
      filename extension).

  --minPWMs <INTEGER>
      Minimum number of PWMs. The options --maxPValue and --minOccurrence
      are ignored. The default is 1.

  --maxPWMs <INTEGER>
      Maximum number of PWMs.

  --maxPValue <FLOAT>
      Maximum p-value of PWMs. This filter is not applied to the top
      minimum number of PWMs (see --minPWMs). The default is 1.0.

  --minOccurrence <FLOAT>
      Minimum fraction of sequences that contain the motif. This filter is
      not applied to the top minimum number of PWMs (see --minPWMs). The
      default is 0.05.

  --rankPWMs <INTEGER> [<INTEGER>...]
      PWM ranks in XXmotif results. The former options to initialize BaMMs
      from PWMs are ignored.

  -k <INTEGER>
      Order. The default is 2.

  -a|--alpha <FLOAT> [<FLOAT>...]
      Order-specific prior strength. The default is 1.0 (for k = 0) and
      20 x 3^(k-1) (for k > 0). The options -b and -g are ignored.

  -b|--beta <FLOAT>
      Calculate order-specific alphas according to beta x gamma^(k-1) (for
      k > 0). The default is 20.0.

  -g|--gamma <FLOAT>
      Calculate order-specific alphas according to beta x gamma^(k-1) (for
      k > 0). The default is 3.0.

  --extend <INTEGER>{1,2}
      Extend BaMMs by adding uniformly initialized positions to the left
      and/or right of initial BaMMs. Invoking e.g. with --extend 0 2 adds
      two positions to the right of initial BaMMs. Invoking with --extend 2
      adds two positions to both sides of initial BaMMs. By default, BaMMs
      are not being extended.

  -K <INTEGER>
      Order. The default is 2.

  -A|--Alpha <FLOAT>
      Prior strength. The default is 10.0.

  -q <FLOAT>
      Prior probability for a positive sequence to contain a motif. The
      default is 0.9.

  -e|--epsilon <FLOAT>
      The EM algorithm is deemed to be converged when the sum over the
      absolute differences in BaMM probabilities from successive EM rounds
      is smaller than epsilon. The default is 0.001.

  --XX-ZOOPS
      Use the zero-or-one-occurrence-per-sequence model (default).

  --XX-MOPS
      Use the multiple-occurrence-per-sequence model.

  --XX-OOPS
      Use the one-occurrence-per-sequence model.

  --XX-seeds ALL|FIVEMERS|PALINDROME|TANDEM|NOPALINDROME|NOTANDEM
      Define the nature of seed patterns. The default is to start using ALL
      seed pattern variants.

  --XX-gaps 0|1|2|3
      Maximum number of gaps used for seed patterns. The default is 0.

  --XX-pseudoCounts <FLOAT>
      Percentage of pseudocounts. The default is 10.0.

  --XX-mergeMotifsThreshold LOW|MEDIUM|HIGH
      Define the similarity threshold used to merge PWMs. The default is to
      merge PWMs with LOW similarity in order to reduce runtime.

  --XX-maxPositions <INTEGER>
      Limit the number of motif positions to reduce runtime. The default is
      17.

  --XX-noLengthOptimPWMs
      Omit the length optimization of PWMs.

  --XX-K <INTEGER>
      Order of the (homogeneous) background BaMM. The default is either 2
      (when learned on positive sequences) or 8 (when learned on background
      sequences).

  --XX-A <FLOAT>
      Prior strength of the (homogeneous) background BaMM. The default is
      10.0.

  --XX-jumpStartPatternStage <STRING>
      Jump-start pattern stage using an IUPAC pattern string.

  --XX-jumpStartPWMStage <FILEPATH>
      Jump-start PWM stage reading in a PWM from file.

  --XX-localization
      Calculate p-values for positional clustering of motif occurrences in
      positive sequences of equal length. Improves the sensitivity to find
      weak but positioned motifs.

  --XX-localizationRanking
      Rank motifs according to localization statistics.

  --XX-downstreamPositions <INTEGER>
      Distance between the anchor position (e.g. the transcription start
      site) and the last positive sequence nucleotide. Corrects motif
      positions in result plots. The default is 0.

  --XX-batch
      Suppress progress bars.

  --scorePosSequenceSet
      Score positive (training) sequences with optimized BaMMs.

  --scoreNegSequenceSet
      Score background (training) sequences with optimized BaMMs.

  --scoreTestSequenceSet <FILEPATH> [<FILEPATH>...]
      Score test sequences with optimized BaMMs. Test sequences can be
      provided in a single or multiple FASTA files.

  --saveInitBaMMs
      Write initialized BaMM(s) to disk.

  --saveBaMMs
      Write optimized BaMM(s) to disk.

  --verbose
      Verbose terminal printouts.

  -h, --help
      Printout this help.

source( "plotBaMM.wrapper.R" )