[med-svn] [Git][med-team/proteinortho][upstream] New upstream version 6.0.31+dfsg
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Tue Jun 22 15:43:15 BST 2021
Nilesh Patra pushed to branch upstream at Debian Med / proteinortho
Commits:
752018a7 by Nilesh Patra at 2021-06-22T20:00:11+05:30
New upstream version 6.0.31+dfsg
- - - - -
6 changed files:
- CHANGELOG
- CHANGEUID
- Makefile
- README.md
- proteinortho6.pl
- src/.gitlab-ci.yml
Changes:
=====================================
CHANGELOG
=====================================
@@ -297,3 +297,5 @@
6. April (5584)
fixed a bug, where generated databases are always overwritten (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/48). Thanks to Bjoern
fixed another bug that caused the compilation of proteinortho_clustering to fail on CentOS (OMP_PROC_BIND=true) (https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/39).
+ 20. Juli (5594)
+ Makefile modification to account for issue 51+52: the -mtune and -march option are now totally optional.
=====================================
CHANGEUID
=====================================
@@ -1 +1 @@
-5584
+5594
=====================================
Makefile
=====================================
@@ -19,6 +19,7 @@
## CXXLIBRARY = the path to the libs like lapack,... (dont forget the -L)
## CXXINCLUDE = include path (^) (dont forget the -I)
## PREFIX = the installation prefix (only for make install)
+## MTUNEARCH = if true then '-march=native -mtune=native'
################################################################
##########################
@@ -31,7 +32,6 @@ INSTALLDIR=/usr/local/bin
USELAPACK=TRUE
# compile statically
STATIC=FALSE
-
DEPLOY=FALSE
ifdef static
@@ -50,9 +50,24 @@ ifdef LAPACK
USELAPACK=$(LAPACK)
endif
+# normalize true and TRUE
+ifeq ($(MTUNEARCH),true)
+MTUNEARCH=TRUE
+endif
ifeq ($(STATIC),true)
STATIC=TRUE
endif
+ifeq ($(USELAPACK),true)
+USELAPACK=TRUE
+endif
+ifeq ($(DEPLOY),true)
+DEPLOY=TRUE
+endif
+
+# set MTUNEARCHFLAGS
+ifeq ($(MTUNEARCH),TRUE)
+MTUNEARCHFLAGS=-march=native -mtune=native
+endif
USEPRECOMPILEDLAPACK=TRUE
@@ -82,7 +97,7 @@ endif
dir_guard=@if [ ! -d $(BUILDDIR) ]; then echo "Creating build directory ..."; mkdir -p $(BUILDDIR); fi
.PHONY: all
-all:$(BUILDDIR)/proteinortho_extract_from_graph.pl $(BUILDDIR)/proteinortho_compareProteinorthoGraphs.pl $(BUILDDIR)/proteinortho_grab_proteins.pl $(BUILDDIR)/proteinortho_formatUsearch.pl $(BUILDDIR)/proteinortho_do_mcl.pl $(BUILDDIR)/proteinortho2tree.pl $(BUILDDIR)/proteinortho2html.pl $(BUILDDIR)/proteinortho2xml.pl $(BUILDDIR)/proteinortho_singletons.pl $(BUILDDIR)/proteinortho_summary.pl $(BUILDDIR)/proteinortho_ffadj_mcs.py $(BUILDDIR)/proteinortho_clustering $(BUILDDIR)/proteinortho_history.pl $(BUILDDIR)/proteinortho_graphMinusRemovegraph $(BUILDDIR)/proteinortho_cleanupblastgraph $(BUILDDIR)/proteinortho_treeBuilderCore
+all:echoENV $(BUILDDIR)/proteinortho_extract_from_graph.pl $(BUILDDIR)/proteinortho_compareProteinorthoGraphs.pl $(BUILDDIR)/proteinortho_grab_proteins.pl $(BUILDDIR)/proteinortho_formatUsearch.pl $(BUILDDIR)/proteinortho_do_mcl.pl $(BUILDDIR)/proteinortho2tree.pl $(BUILDDIR)/proteinortho2html.pl $(BUILDDIR)/proteinortho2xml.pl $(BUILDDIR)/proteinortho_singletons.pl $(BUILDDIR)/proteinortho_summary.pl $(BUILDDIR)/proteinortho_ffadj_mcs.py $(BUILDDIR)/proteinortho_clustering $(BUILDDIR)/proteinortho_history.pl $(BUILDDIR)/proteinortho_graphMinusRemovegraph $(BUILDDIR)/proteinortho_cleanupblastgraph $(BUILDDIR)/proteinortho_treeBuilderCore
@echo "[100%] $(GREEN)Everything is compiled with no errors.$(NC)"
$(BUILDDIR)/proteinortho_extract_from_graph.pl: src/proteinortho_extract_from_graph.pl
@@ -142,10 +157,16 @@ echoENV:
@echo $(CXX)
@echo -n "CXXFLAGS = "
@echo $(CXXFLAGS)
+ @echo -n "MTUNEARCHFLAGS = "
+ @echo $(MTUNEARCHFLAGS)
@echo -n "LDFLAGS = "
@echo $(LDFLAGS)
@echo -n "LDLIBS = "
@echo $(LDLIBS)
+ @echo -n "STATIC = "
+ @echo $(STATIC)
+ @echo -n "USELAPACK = "
+ @echo $(USELAPACK)
# 1. Try to compile statically with LAPACK
# 2. try to compile dynamically with the given lapack lib in src/
@@ -155,47 +176,43 @@ $(BUILDDIR)/proteinortho_clustering: src/proteinortho_clustering.cpp
@echo "[ 10%] Prepare proteinortho_clustering ..."
ifeq ($(DEPLOY),TRUE)
- @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking, no mtune,march , for gitlab)";
- @echo "$(CXX) -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] )
+ @echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking, no mtune,march , for gitlab)";
+ @echo "$(CXX) -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] )
else
ifeq ($(USELAPACK),TRUE)
ifeq ($(USEPRECOMPILEDLAPACK),TRUE)
ifeq ($(STATIC),TRUE)
@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (static linking)";
- @echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] ) || ( \
+ @echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] ) || ( \
echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive... (this should now work for OSX).$(NC)"; \
- echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
- echo "......$(ORANGE)-march=native -mtune=native failed, I try without them again.$(NC)"; \
- echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] ) || ( \
+ echo "$(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath" && $(CXX) -O2 -static $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -Wl,--allow-multiple-definition -llapack -lblas -lgfortran -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -lquadmath && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] ) || ( \
echo "......$(ORANGE)static linking failed, now I try dynamic linking.$(NC)"; \
- echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).$(NC)"; \
- echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......$(ORANGE)dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.$(NC)"; \
- echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......$(ORANGE)last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.$(NC)"; \
echo "......[ 33%] Extracting the LAPACK library"; \
if [ ! -d src/lapack-3.8.0 ]; then echo "cd src; tar -xzvf lapack-3.8.0.tar.gz"; cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
echo "......[ 66%] Compiling the LAPACK library (using cmake + make)"; \
if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then echo " mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 "; mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \
echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \
- echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) ) ) )
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) ) )
else
@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";
- @echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -march=native -mtune=native -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
- echo "......$(ORANGE)-march=native -mtune=native failed, I try without them again.$(NC)"; \
- echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ @echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -Wl,--whole-archive -lpthread -Wl,--no-whole-archive && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......$(ORANGE)dynamic linking failed too, now I try dynamic linking without -WL,-whole-archive (this should now work for OSX).$(NC)"; \
- echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -llapack -lblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......$(ORANGE)dynamic linking failed (without -WL,-whole-archive) too too, now I try to openblas.$(NC)"; \
- echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< $(LDFLAGS) $(LDLIBS) -lopenblas -pthread -lpthread && ([ $$? -eq 0 ] && $@ -test && [ $$? -eq 0 ] && echo "......OK dynamic linking was successful for proteinortho_clustering!";) || ( \
echo "......$(ORANGE)last linking failed too too too, now I try to recompile lapack (v.3.8.0) and then compile proteinortho_clustering with dynamic linking.$(NC)"; \
echo "......[ 33%] Extracting the LAPACK library"; \
if [ ! -d src/lapack-3.8.0 ]; then echo "cd src; tar -xzvf lapack-3.8.0.tar.gz"; cd src; tar -xzvf lapack-3.8.0.tar.gz > /dev/null 2>&1; cd ..; fi; \
echo "......[ 66%] Compiling the LAPACK library (using cmake + make)"; \
if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then echo "mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4"; mkdir src/lapack-3.8.0/build 2> /dev/null; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi; \
echo "......[ 99%] Building **proteinortho_clustering** with LAPACK (dynamic linking)"; \
- echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) ) )
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran && echo "......OK dynamic linking was successful for proteinortho_clustering!" || ( echo "" ) ; ) ) )
endif
@if [ ! -e $(BUILDDIR)/proteinortho_clustering ]; then echo "proteinortho_clustering compilation failed. Please visit https://gitlab.com/paulklemm_PHD/proteinortho/wikis/Error%20Codes"; false; fi
else
@@ -204,14 +221,14 @@ else
@echo "[ 18%] Compiling the LAPACK library (using cmake + make)";
@if [ ! -f src/lapack-3.8.0/build/lib/liblapack.a ]; then echo "mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX); make all -j4"; mkdir src/lapack-3.8.0/build; cd src/lapack-3.8.0/build; cmake .. -DCMAKE_CXX_COMPILER=$(CXX) > /dev/null 2>&1; make all -j4 > /dev/null 2>&1; cd ../../.. ; fi;
@echo "[ 20%] Building **proteinortho_clustering** with LAPACK (dynamic linking)";
- @echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran;
+ @echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ $< -Isrc/lapack-3.8.0/build/include/ -Lsrc/lapack-3.8.0/build/lib/ -llapack -lblas $(LDFLAGS) $(LDLIBS) -lgfortran;
endif
endif
ifeq ($(USELAPACK),FALSE)
@echo "[ 20%] Building **proteinortho_clustering** WITHOUT(!) LAPACK";
- @echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+ @echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
echo "......$(ORANGE)static linking failed of proteinortho_clustering_nolapack, now i switch to dynamic linking.$(NC)"; \
- echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS)" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful for proteinortho_clustering_nolapack!"; )
+ echo "$(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS)" && $(CXX) -O2 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -fopenmp -o $@ src/proteinortho_clustering_nolapack.cpp $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful for proteinortho_clustering_nolapack!"; )
endif
endif
@@ -219,22 +236,22 @@ $(BUILDDIR)/proteinortho_cleanupblastgraph: src/cleanupblastgraph.cpp
$(dir_guard)
@echo "[ 50%] Building **cleanupblastgraph**"
ifeq ($(STATIC),TRUE)
- @echo "$(CXX) -std=c++11 $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static" && $(CXX) -std=c++11 $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+ @echo "$(CXX) -std=c++11 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static" && $(CXX) -std=c++11 $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
echo "......$(ORANGE)static linking failed of cleanupblastgraph, now i switch to dynamic linking.$(NC)"; \
- echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful of cleanupblastgraph!"; )
+ echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) && echo "......OK dynamic linking was successful of cleanupblastgraph!"; )
else
- @echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
+ @echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
endif
$(BUILDDIR)/proteinortho_graphMinusRemovegraph: src/graphMinusRemovegraph.cpp
$(dir_guard)
@echo "[ 25%] Building **graphMinusRemovegraph**"
ifeq ($(STATIC),TRUE)
- @echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
+ @echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS) -static && ([ $$? -eq 0 ] ) || ( \
echo "......$(ORANGE)static linking failed of graphMinusRemovegraph, now i switch to dynamic linking.$(NC)"; \
- echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $<" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< && echo "......OK dynamic linking was successful of graphMinusRemovegraph!"; )
+ echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $<" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< && echo "......OK dynamic linking was successful of graphMinusRemovegraph!"; )
else
- @echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
+ @echo "$(CXX) $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)" && $(CXX) $(CPPFLAGS) $(CXXFLAGS) $(MTUNEARCHFLAGS) -o $@ $< $(LDFLAGS) $(LDLIBS)
endif
$(BUILDDIR)/proteinortho_treeBuilderCore: src/po_tree.c
=====================================
README.md
=====================================
@@ -486,7 +486,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/
<br>
**Synteny options (optional, step 2)**
- (output: <myproject>.ffadj-graph, <myproject>.poff.tsv (tab separated file)-graph)
+ (output: <myproject>.ffadj-graph, <myproject>.poff-graph, <myproject>.poff.tsv (tab separated file with groups))
<details>
<summary>More (Click to expand)</summary>
@@ -698,7 +698,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/
**POFF (-synteny)**
The synteny based graph files (myproject.ffadj-graph and
- myproject.poff.tsv (tab separated file)-graph) have two additional columns: same_strand and
+ myproject.poff-graph) have two additional columns: same_strand and
simscore. The first one indicates if two genes from a match are located at
the same strands (1) or not (-1). The second one is an internal score
which can be interpreted as a normalized weight ranging from 0 to 1 based
@@ -718,7 +718,7 @@ Open `proteinorthoHelper.html` in your favorite browser or visit [lechnerlab.de/
<br>
<details>
- <summary>myproject.poff.tsv (tab separated file)-graph (Click to expand)</summary>
+ <summary>myproject.poff-graph (Click to expand)</summary>
clustered ffadj graph. Its connected components are represented in
myproject.poff.tsv (tab separated file) (only if -synteny is set)
=====================================
proteinortho6.pl
=====================================
@@ -473,7 +473,7 @@ use POSIX;
##########################################################################################
# Variables
##########################################################################################
-our $version = "6.0.30";
+our $version = "6.0.31";
our $step = 0; # 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3
our $verbose = 1; # 0/1 -> don't / be verbose
our $debug = 0; # 0/1 -> don't / show debug data
=====================================
src/.gitlab-ci.yml
=====================================
@@ -235,34 +235,34 @@ debian-latest:
# - export PATH="$PATH:$HOME"
# - echo "start proteinortho tests"
-centos-latest:
- image: centos
- stage: recompile-and-test
- script:
- - yum -y groupinstall "Development Tools"
- - yum -y install gcc-c++
- - yum -y install cmake
- - yum -y install make
- - yum -y install tar
- - yum -y install which
- - yum -y install wget
- - yum -y install gcc-gfortran python3
- - wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast*-x64-linux.tar.gz
- - tar -xzvf ncbi-blast*-x64-linux.tar.gz
- - cp ncbi-blast*/bin/blastp $HOME
- - cp ncbi-blast*/bin/makeblastdb $HOME
- - echo "installing diamond"
- - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
- - tar xzf diamond-linux64.tar.gz
- - cp diamond $HOME
- - export PATH="$PATH:$HOME"
- - echo "start proteinortho tests"
- - make clean
- - make
- - make test
- - perl proteinortho*pl test/*faa || exit 1
- - rm *info;
- - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
+#centos-latest:
+# image: centos
+# stage: recompile-and-test
+# script:
+# - yum -y groupinstall "Development Tools"
+# - yum -y install gcc-c++
+# - yum -y install cmake
+# - yum -y install make
+# - yum -y install tar
+# - yum -y install which
+# - yum -y install wget
+# - yum -y install gcc-gfortran python3 atlas atlas-devel lapack blas
+# - wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast*-x64-linux.tar.gz
+# - tar -xzvf ncbi-blast*-x64-linux.tar.gz
+# - cp ncbi-blast*/bin/blastp $HOME
+# - cp ncbi-blast*/bin/makeblastdb $HOME
+# - echo "installing diamond"
+# - wget http://github.com/bbuchfink/diamond/releases/download/v2.0.6/diamond-linux64.tar.gz
+# - tar xzf diamond-linux64.tar.gz
+# - cp diamond $HOME
+# - export PATH="$PATH:$HOME"
+# - echo "start proteinortho tests"
+# - make clean
+# - make
+# - make test
+# - perl proteinortho*pl test/*faa || exit 1
+# - rm *info;
+# - for f in myproject.*; do if [ "$(grep -v '#' $f | wc -l | awk '{print $1}' | tr -d '\n')" -lt 10 ]; then echo "$f failed size check, output should be more than 10 lines..."; exit 1; fi; done
#code_quality:
# image: docker:stable
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/commit/752018a7f58833804dcab4f526edf1d87c2a8863
--
View it on GitLab: https://salsa.debian.org/med-team/proteinortho/-/commit/752018a7f58833804dcab4f526edf1d87c2a8863
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