GitHub - bmajoros/BOOM: Bioinformatics Object Oriented Modules

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 186 Commits
GSL		GSL
TNT		TNT
lambda		lambda
AdjacencyGraph.C		AdjacencyGraph.C
AdjacencyGraph.H		AdjacencyGraph.H
Alignment.C		Alignment.C
Alignment.H		Alignment.H
AlignmentSeq.C		AlignmentSeq.C
AlignmentSeq.H		AlignmentSeq.H
AlignmentTrack.C		AlignmentTrack.C
AlignmentTrack.H		AlignmentTrack.H
Alphabet.C		Alphabet.C
Alphabet.H		Alphabet.H
AlphabetMap.C		AlphabetMap.C
AlphabetMap.H		AlphabetMap.H
AminoAlphabet.C		AminoAlphabet.C
AminoAlphabet.H		AminoAlphabet.H
ApproximateAlignment.C		ApproximateAlignment.C
ApproximateAlignment.H		ApproximateAlignment.H
Array1D.H		Array1D.H
Array1DSorter.H		Array1DSorter.H
Array2D.H		Array2D.H
Array3D.H		Array3D.H
BandedAlignmentMatrix.H		BandedAlignmentMatrix.H
BandedMatrix3D.C		BandedMatrix3D.C
BandedMatrix3D.H		BandedMatrix3D.H
BandedSmithWaterman.H		BandedSmithWaterman.H
Bed3Record.C		Bed3Record.C
Bed3Record.H		Bed3Record.H
BinaryAlphabet.C		BinaryAlphabet.C
BinaryAlphabet.H		BinaryAlphabet.H
BinaryTree.H		BinaryTree.H
BinomialDistribution.C		BinomialDistribution.C
BinomialDistribution.H		BinomialDistribution.H
BitSet.C		BitSet.C
BitSet.H		BitSet.H
BoundedSortedArray.H		BoundedSortedArray.H
CFasta.C		CFasta.C
CFasta.H		CFasta.H
Chi2FitTest.C		Chi2FitTest.C
Chi2FitTest.H		Chi2FitTest.H
Chi2IndepTest.C		Chi2IndepTest.C
Chi2IndepTest.H		Chi2IndepTest.H
Chi2Table.C		Chi2Table.C
Chi2Table.H		Chi2Table.H
CigarAlignment.C		CigarAlignment.C
CigarAlignment.H		CigarAlignment.H
CigarString.C		CigarString.C
CigarString.H		CigarString.H
CodonIterator.C		CodonIterator.C
CodonIterator.H		CodonIterator.H
CombinationIterator.C		CombinationIterator.C
CombinationIterator.H		CombinationIterator.H
CommandLine.C		CommandLine.C
CommandLine.H		CommandLine.H
Comparator.H		Comparator.H
ComplexNum.C		ComplexNum.C
ComplexNum.H		ComplexNum.H
ConfigFile.C		ConfigFile.C
ConfigFile.H		ConfigFile.H
Constants.H		Constants.H
ContingencyTbl.C		ContingencyTbl.C
ContingencyTbl.H		ContingencyTbl.H
ContinuousDistr.H		ContinuousDistr.H
Correlation.C		Correlation.C
Correlation.H		Correlation.H
Cypher.C		Cypher.C
Cypher.H		Cypher.H
DblMatrix.C		DblMatrix.C
DblMatrix.H		DblMatrix.H
DegenerateDnaAlphabet.C		DegenerateDnaAlphabet.C
DegenerateDnaAlphabet.H		DegenerateDnaAlphabet.H
Direction.H		Direction.H
DiscreteDistr.H		DiscreteDistr.H
DiscreteLogDistr.H		DiscreteLogDistr.H
DnaAlphabet.C		DnaAlphabet.C
DnaAlphabet.H		DnaAlphabet.H
DnaAlphabetWithGaps.C		DnaAlphabetWithGaps.C
DnaAlphabetWithGaps.H		DnaAlphabetWithGaps.H
DnaDashAlphabet.C		DnaDashAlphabet.C
DnaDashAlphabet.H		DnaDashAlphabet.H
DnaDashDotAlphabet.C		DnaDashDotAlphabet.C
DnaDashDotAlphabet.H		DnaDashDotAlphabet.H
DnaSubstitutionMatrix.C		DnaSubstitutionMatrix.C
DnaSubstitutionMatrix.H		DnaSubstitutionMatrix.H
EdgeWeights.C		EdgeWeights.C
EdgeWeights.H		EdgeWeights.H
EdgeWeightsMatrix.C		EdgeWeightsMatrix.C
EdgeWeightsMatrix.H		EdgeWeightsMatrix.H
ElasVector.C		ElasVector.C
ElasVector.H		ElasVector.H
Entropy.C		Entropy.C
Entropy.H		Entropy.H
Environment.C		Environment.C
Environment.H		Environment.H
Essex.C		Essex.C
Essex.H		Essex.H
Exceptions.C		Exceptions.C
Exceptions.H		Exceptions.H
ExtremeValueDistribution.C		ExtremeValueDistribution.C

Repository files navigation

To compile:

1. Set your environment variable GSLDIR to the pull path to the 
   Gnu Scientific Library; this directory should have subdirectories
   called bin, include, and lib.  Also set your LIBRARY_PATH and
   LD_LIBRARY_PATH environment variables to the full path to the lib
   subdirectory of GSL.  For example:
      setenv GSLDIR /home/wmajoros/gsl
      setenv LIBRARY_PATH /home/wmajoros/gsl/lib
      setenv LD_LIBRARY_PATH /home/wmajoros/gsl/lib

2. In the BOOM/GSL subdirectory, create a symbolic link to the
   parent directory, and call it BOOM:
       cd BOOM/GSL ; ln -s .. BOOM ; cd -

3. Type "make libBOOM.a"