Author: Steffen Möller
Last-Update: 2018-06-17 20:25:27 +0200
Description: Work around issues with creating manpage, use Debian packaged libs

--- a/Makefile.am
+++ b/Makefile.am
@@ -1,5 +1,5 @@
 ACLOCAL_AMFLAGS = -I m4
-SUBDIRS = libs igor_src
+SUBDIRS = igor_src
 
 # modelsdir = $(pkgdatadir) 
 # models_DATA = models demo
@@ -10,7 +10,7 @@ demodir = $(pkgdatadir)/demo
 demo_DATA = demo/genomicVs_with_primers.fasta demo/genomicDs.fasta demo/genomicJs_all_curated.fasta demo/murugan_naive1_noncoding_demo_seqs.txt
 
 #Install the generated man pages
-man_MANS = igor.1
+#man_MANS = igor.1
 
 # Scripts
 bin_SCRIPTS = \
--- a/configure.ac
+++ b/configure.ac
@@ -36,9 +36,6 @@ AC_TYPE_SIZE_T
 AC_CHECK_FUNCS([pow sqrt])
 
 AC_CONFIG_FILES([Makefile
-                 igor_src/Makefile
-                 libs/Makefile])
-AC_CONFIG_SUBDIRS([libs/gsl_sub
-                   libs/jemalloc
-					igor_src])
+                 igor_src/Makefile])
+AC_CONFIG_SUBDIRS([ igor_src])
 AC_OUTPUT
--- a/igor_src/Makefile.am
+++ b/igor_src/Makefile.am
@@ -11,11 +11,9 @@ igor_SOURCES = $(SOURCES) main.cpp
 
 # Include GSL subparts and jemalloc without installation
 
-igor_LDADD = ../libs/gsl_sub/libgsl_sub.la ../libs/jemalloc/lib/libjemalloc.a -lpthread -ldl #Need to link pthread since it is not statically linked with jemalloc (for now)
-
-
-igor_CXXFLAGS = -I$(srcdir)/../libs/jemalloc/include/jemalloc -I$(srcdir)/../libs/gsl_sub $(OPENMP_CXXFLAGS) -DIGOR_DATA_DIR=\"$(pkgdatadir)\"
+igor_LDADD = -lgsl -lblas -ljemalloc -lpthread -ldl #Need to link pthread since it is not statically linked with jemalloc (for now)
 
+igor_CXXFLAGS = -I/usr/include/jemalloc -I/usr/include/gsl $(OPENMP_CXXFLAGS) -DIGOR_DATA_DIR=\"$(pkgdatadir)\"
 
 # Pass IGoR data install directory path through the compiler with -DIGOR_DATA_DIR=\"$(pkgdatadir)\"
 # and not in config.h (as it is best practice according to: https://stackoverflow.com/questions/5867136/autoconf-how-to-get-installation-paths-into-config-h#11317815)