Fixed docker build and unittests

Author: agraubert

Dockerfile

@@ -24,7 +24,7 @@ RUN apt-get update && apt-get install -y software-properties-common && \
 COPY Makefile /opt/rnaseqc/Makefile
 RUN cd /opt/rnaseqc && git clone --recursive https://github.com/walaj/SeqLib.git && \
     cd SeqLib && git checkout 7e1f98267b5057f9505dbff119308137a0e006db && cd .. && \
-    make SeqLib/bin/libseqlib.a
+    make SeqLib/lib/libseqlib.a
 
 # python
 RUN cd /opt && git clone https://github.com/francois-a/rnaseq-utils rnaseq && cd rnaseq && \

Makefile

@@ -17,7 +17,7 @@ SRCDIR=src
 OBJECTS=$(SOURCES:.cpp=.o)
 SEQFLAGS=$(STDLIB) -D_GLIBCXX_USE_CXX11_ABI=$(ABI)
 
-rnaseqc: $(foreach file,$(OBJECTS),$(SRCDIR)/$(file)) SeqLib/bin/libseqlib.a SeqLib/bin/libhts.a
+rnaseqc: $(foreach file,$(OBJECTS),$(SRCDIR)/$(file)) SeqLib/lib/libseqlib.a SeqLib/lib/libhts.a
 	$(CC) -O3 $(LIBRARY_PATHS) -o $@ $^ $(STATIC_LIBS) $(LIBS)
 
 .PHONY: lib
@@ -28,7 +28,7 @@ lib: $(foreach file,$(OBJECTS),$(SRCDIR)/$(file))
 %.o: %.cpp
 	$(CC) $(CFLAGS) -I. $(INCLUDE_DIRS) -c -o $@ $<
 
-SeqLib/bin/libseqlib.a SeqLib/bin/libhts.a:
+SeqLib/lib/libseqlib.a SeqLib/lib/libhts.a:
 	cd SeqLib && ./configure && make CXXFLAGS="$(SEQFLAGS)" && make install
 
 .PHONY: clean

test_data/Makefile.linux

@@ -5,7 +5,7 @@ LIBRARY_PATHS=
 #Set to 0 if you encounter linker errors regarding strings from the bamtools library
 ABI=1
 #Provide full paths here to .a archives for libraries which should be statically linked
-STATIC_LIBS=SeqLib/bin/libhts.a /usr/lib/x86_64-linux-gnu/libboost_filesystem.a /usr/lib/x86_64-linux-gnu/libboost_regex.a /usr/lib/x86_64-linux-gnu/libboost_system.a /usr/lib/x86_64-linux-gnu/libz.a /usr/lib/x86_64-linux-gnu/liblzma.a /usr/lib/x86_64-linux-gnu/libbz2.a /usr/lib/gcc/x86_64-linux-gnu/5.5.0/libstdc++.a
+STATIC_LIBS=SeqLib/lib/libhts.a /usr/lib/x86_64-linux-gnu/libboost_filesystem.a /usr/lib/x86_64-linux-gnu/libboost_regex.a /usr/lib/x86_64-linux-gnu/libboost_system.a /usr/lib/x86_64-linux-gnu/libz.a /usr/lib/x86_64-linux-gnu/liblzma.a /usr/lib/x86_64-linux-gnu/libbz2.a /usr/lib/gcc/x86_64-linux-gnu/5.5.0/libstdc++.a
 #List of remaining libraries that will be dynamically linked
 LIBS=-lpthread
 
@@ -16,13 +16,13 @@ SOURCES=BED.cpp Expression.cpp GTF.cpp RNASeQC.cpp Metrics.cpp Fasta.cpp BamRead
 SRCDIR=src
 OBJECTS=$(SOURCES:.cpp=.o)
 
-rnaseqc: $(foreach file,$(OBJECTS),$(SRCDIR)/$(file)) SeqLib/bin/libseqlib.a SeqLib/bin/libhts.a
+rnaseqc: $(foreach file,$(OBJECTS),$(SRCDIR)/$(file)) SeqLib/lib/libseqlib.a SeqLib/lib/libhts.a
 	$(CC) -static -static-libstdc++ -static-libgcc -O3 $(LIBRARY_PATHS) -o $@ $^ $(STATIC_LIBS) $(LIBS)
 
 %.o: %.cpp
 	$(CC) -static -static-libstdc++ -static-libgcc $(CFLAGS) -I. $(INCLUDE_DIRS) -c -o $@ $<
 
-SeqLib/bin/libseqlib.a SeqLib/bin/libhts.a:
+SeqLib/lib/libseqlib.a SeqLib/lib/libhts.a:
 	cd SeqLib && ./configure && make CXXFLAGS=$(STDLIB) && make install
 
 .PHONY: clean

test_data/Makefile.osx

@@ -5,7 +5,7 @@ LIBRARY_PATHS=
 #Set to 0 if you encounter linker errors regarding strings from the bamtools library
 ABI=1
 #Provide full paths here to .a archives for libraries which should be statically linked
-STATIC_LIBS=/usr/local/lib/libboost_filesystem.a /usr/local/lib/libboost_regex.a /usr/local/lib/libboost_system.a $(ZLIB_PATH) SeqLib/bin/libhts.a $(LZMA_PATH) /usr/local/opt/bzip2/lib/libbz2.a
+STATIC_LIBS=/usr/local/lib/libboost_filesystem.a /usr/local/lib/libboost_regex.a /usr/local/lib/libboost_system.a $(ZLIB_PATH) SeqLib/lib/libhts.a $(LZMA_PATH) /usr/local/opt/bzip2/lib/libbz2.a
 #List of remaining libraries that will be dynamically linked
 LIBS=
 
@@ -16,13 +16,13 @@ SOURCES=BED.cpp Expression.cpp GTF.cpp RNASeQC.cpp Metrics.cpp Fasta.cpp BamRead
 SRCDIR=src
 OBJECTS=$(SOURCES:.cpp=.o)
 
-rnaseqc: $(foreach file,$(OBJECTS),$(SRCDIR)/$(file)) SeqLib/bin/libseqlib.a SeqLib/bin/libhts.a
+rnaseqc: $(foreach file,$(OBJECTS),$(SRCDIR)/$(file)) SeqLib/lib/libseqlib.a SeqLib/lib/libhts.a
 	$(CC) -O3 $(LIBRARY_PATHS) -o $@ $^ $(STATIC_LIBS) $(LIBS)
 
 %.o: %.cpp
 	$(CC) $(CFLAGS) -I. $(INCLUDE_DIRS) -c -o $@ $<
 
-SeqLib/bin/libseqlib.a SeqLib/bin/libhts.a:
+SeqLib/lib/libseqlib.a SeqLib/lib/libhts.a:
 	cd SeqLib && ./configure && make CXXFLAGS=$(STDLIB) && make install
 
 .PHONY: clean