Commit 197b5749 authored by LANORE Vincent's avatar LANORE Vincent
Browse files

Corrections to msd files and makefile so it compiles. Msd dockerfile now works.

parent 9af451f2
......@@ -23,7 +23,7 @@
#include <stdlib.h>
#include <math.h>
#include <cblas.h>
/* #include <cblas.h> */
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_math.h>
#include <gsl/gsl_eigen.h>
......
......@@ -10,12 +10,12 @@ OBJ_ENR = StatAnnotation.o Annotation.o Utils.o Enrichment.o
# compiler and its options
CC = gcc
CFLAGS = -I/usr/local/include -I/usr/include -Wall -Wno-char-subscripts -D_POSIX_SOURCE -std=c99 -Wall -pedantic -march=native -O3
CFLAGS = -I/usr/local/include -I/usr/include -Wall -Wno-char-subscripts -D_POSIX_SOURCE -std=c99 -Wall -pedantic -O3
# linker and its options
LD = $(CC)
LDFLAGS = -rdynamic -lm /usr/local/lib/libnlopt.a -lgsl -lgslcblas
LDFLAGS_TH = -rdynamic -lm /usr/local/lib/libnlopt.a -lgsl -lgslcblas -D_REENTRANT -L/usr/local/lib -L/usr/lib/ -lpthread
LDFLAGS = -rdynamic -lm -lnlopt -lgsl -lgslcblas
LDFLAGS_TH = -rdynamic -lm -lnlopt -lgsl -lgslcblas -D_REENTRANT -L/usr/local/lib -L/usr/lib/ -lpthread
############ LIST OF EXECUTABLE TARGETS (MODIFY ONLY TO ADD AN EXECUTABLE) ##############
......
AATree.o: AATree.c AATree.h
Alignment.o: Alignment.c Utils.h Alignment.h
AlignmentLikelihood.o: AlignmentLikelihood.c AlignmentLikelihood.h \
Alignment.h Tree.h Utils.h EvolutionModel.h ColumnLikelihood.h \
EvolutionModelProt.h EvolutionModelProtStored.h NLOpt.h
Annotation.o: Annotation.c Utils.h Annotation.h
Character.o: Character.c Character.h Utils.h
ColumnLikelihood.o: ColumnLikelihood.c ColumnLikelihood.h Tree.h Utils.h \
EvolutionModel.h
ConvergenceExpectation.o: ConvergenceExpectation.c Utils.h \
ConvergenceExpectation.h EvolutionModel.h Tree.h ColumnLikelihood.h \
NLOpt.h EvolutionModelProtStored.h EvolutionModelProt.h
DensityUtils.o: DensityUtils.c DensityUtils.h
Enrichment.o: Enrichment.c Utils.h Annotation.h StatAnnotation.h
EvolutionModel.o: EvolutionModel.c EvolutionModel.h
EvolutionModelProt.o: EvolutionModelProt.c EvolutionModelProt.h \
EvolutionModel.h
EvolutionModelProtStored.o: EvolutionModelProtStored.c \
EvolutionModelProtStored.h Tree.h Utils.h EvolutionModel.h \
EvolutionModelProt.h
MolSigDetect.o: MolSigDetect.c Tree.h Utils.h Alignment.h Character.h \
EvolutionModel.h EvolutionModelProt.h EvolutionModelProtStored.h \
ConvergenceExpectation.h ColumnLikelihood.h AlignmentLikelihood.h \
NLOpt.h DensityUtils.h AATree.h
NLOpt.o: NLOpt.c NLOpt.h
StatAnnotation.o: StatAnnotation.c Utils.h StatAnnotation.h Annotation.h
Tree.o: Tree.c Tree.h Utils.h
Utils.o: Utils.c Utils.h
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