profuse/Jamroot at master · galosh/profuse · GitHub

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project profuse
    : requirements <library>/HMMoC-BFloat-Algebra//libHMMoC-BFloat-Algebra
    : requirements <warnings>off ;

use-project /HMMoC-BFloat-Algebra : ./HMMoC-BFloat-Algebra ;

exe profileToAlignmentProfile_AA
    : [ obj profileToAlignmentProfile_AA_obj : profileToAlignmentProfile.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include <define>__PROFUSE_USE_AMINOS ] boost_serialization boost_system boost_graph boost_program_options : ;

exe profileToAlignmentProfile_DNA
    : [ obj profileToAlignmentProfile_DNA_obj : profileToAlignmentProfile.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include ] boost_serialization boost_system boost_graph boost_program_options : ;


alias profileToAlignmentProfile : profileToAlignmentProfile_AA profileToAlignmentProfile_DNA ;

exe align_AA
    : [ obj Align_obj : Align.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include <define>__PROFUSE_USE_AMINOS ] boost_serialization boost_system boost_graph boost_program_options : ;

exe align_DNA
    : [ obj Align_obj : Align.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include ] boost_serialization boost_system boost_graph boost_program_options : ;

alias align : align_AA align_DNA ;


exe score_AA
    : [ obj Score_obj : Score.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include <define>__PROFUSE_USE_AMINOS ] boost_serialization boost_system boost_graph boost_program_options : ;

exe score_DNA
    : [ obj Score_obj : Score.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include ] boost_serialization boost_system boost_graph boost_program_options : ;

alias score : score_AA score_DNA ;


exe drawSequences_AA
    : [ obj DrawSequences_obj : DrawSequences.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include <define>__PROFUSE_USE_AMINOS ] boost_serialization boost_program_options : ;

exe drawSequences_DNA
    : [ obj DrawSequences_obj : DrawSequences.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include ] boost_serialization boost_program_options : ;

alias drawSequences : drawSequences_AA drawSequences_DNA ;


exe createRandomSequence_DNA
    : [ obj CreateRandomSequence_obj : CreateRandomSequence.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include ] boost_serialization boost_program_options : ;

alias createRandomSequence : createRandomSequence_DNA ;


exe profileCrossEntropy_AA
    : [ obj ProfileCrossEntropy_obj : ProfileCrossEntropy.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include <define>__PROFUSE_USE_AMINOS ] boost_serialization : ;

exe profileCrossEntropy_DNA
    : [ obj ProfileCrossEntropy_obj : ProfileCrossEntropy.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include ] boost_serialization : ;

alias profileCrossEntropy : profileCrossEntropy_AA profileCrossEntropy_DNA ;


alias progs : align score drawSequences createRandomSequence profileCrossEntropy ;


exe sequenceToProfile_AA
    : [ obj SequenceToProfile_obj : SequenceToProfile.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include <define>__PROFUSE_USE_AMINOS ] boost_serialization boost_system boost_graph boost_program_options : ;

exe sequenceToProfile_DNA
    : [ obj SequenceToProfile_obj : SequenceToProfile.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include ] boost_serialization boost_system boost_graph boost_program_options : ;

alias sequenceToProfile : sequenceToProfile_AA sequenceToProfile_DNA ;


exe profileToSequence_AA
    : [ obj ProfileToConsensus_obj : ProfileToConsensus.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include <define>__PROFUSE_USE_AMINOS ] boost_serialization : ;

exe profileToSequence_DNA
    : [ obj ProfileToConsensus_obj : ProfileToConsensus.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include ] boost_serialization : ;

alias profileToSequence : profileToSequence_AA profileToSequence_DNA ;


# exe profileTreeToProfile_AA
#     : [ obj ProfileTreeToProfile_obj : ProfileTreeToProfile.cpp
#         : <include>./prolific <include>./boost-include <include>./seqan-trunk/include <define>__PROFUSE_USE_AMINOS ] boost_serialization boost_system boost_graph boost_program_options boost_filesystem : ;
#
# exe profileTreeToProfile_DNA
#     : [ obj ProfileTreeToProfile_obj : ProfileTreeToProfile.cpp
#         : <include>./prolific <include>./boost-include <include>./seqan-trunk/include ] boost_serialization boost_system boost_graph boost_program_options boost_filesystem : ;
#
# alias profileTreeToProfile : profileTreeToProfile_AA profileTreeToProfile_DNA ;


exe alignedFastaToProfile_AA
    : [ obj AlignedFastaToProfile_obj : AlignedFastaToProfile.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include <define>__PROFUSE_USE_AMINOS ] boost_serialization boost_system boost_graph boost_program_options : ;

exe alignedFastaToProfile_DNA
    : [ obj AlignedFastaToProfile_obj : AlignedFastaToProfile.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include ] boost_serialization boost_system boost_graph boost_program_options : ;

alias alignedFastaToProfile : alignedFastaToProfile_AA alignedFastaToProfile_DNA ;


#alias converters : sequenceToProfile profileToSequence profileTreeToProfile alignedFastaToProfile profileToAlignmentProfile ;
alias converters : sequenceToProfile profileToSequence alignedFastaToProfile profileToAlignmentProfile ;


exe profileToHMMer_DNA
    : [ obj ProfileToHMMer_obj : ProfileToHMMer.cpp
        : <include>./prolific <include>./boost-include <include>./seqan-trunk/include <include>./hmmer/src <include>./hmmer/squid ] boost_serialization boost_system hmmer squid : ;

alias profileToHMMer : profileToHMMer_DNA ;

install dist : progs converters : <location>dist ;

alias install : dist ;

explicit profileToHMMer profileToHMMer_DNA install dist ;

#lib hmmer : : <file>hmmer/src/libhmmer.a ;
#lib squid : : <file>hmmer/squid/libsquid.a ;

## If you are on a multithreaded system, see below
# lib boost_serialization : : <file>./boost-lib/libboost_serialization.a ;
# lib boost_filesystem : : <file>./boost-lib/libboost_filesystem.a ;
# lib boost_graph : : <file>./boost-lib/libboost_graph.a ;
# lib boost_system : : <file>./boost-lib/libboost_system.a ;
# lib boost_program_options : : <file>./boost-lib/libboost_program_options.a ;

## If you are on a multithreaded system, comment out the above and uncomment this:
lib boost_serialization : : <file>./boost-lib/libboost_serialization-mt.dylib ;
lib boost_filesystem : : <file>./boost-lib/libboost_filesystem-mt.dylib ;
lib boost_graph : : <file>./boost-lib/libboost_graph-mt.dylib ;
lib boost_system : : <file>./boost-lib/libboost_system-mt.dylib ;
lib boost_program_options : : <file>./boost-lib/libboost_program_options-mt.dylib ;