Bioconda compatibility fixes.

README.md

@@ -14,11 +14,11 @@
 
 Progressive algorithm for large-scale multiple sequence alignments.
 
-## New features in FAMSA 2 release candidate
+## New features in FAMSA 2
 In version 2.0.0-rc the following important changes have been introduced:
 * Fast guide tree heuristic called Medoid Tree (`-medoidtree` switch) for ultra-scale alignments:
   * the entire Pfam-A v33.1 in its largest NCBI variant (over 18 thousand families, 60 GB of raw FASTA files) was analyzed in 8 hours,	
-  * the famility PF00005 of 3 million ABC transporters was aligned in 5 minutes and 24 GB of RAM.
+  * the family PF00005 of 3 million ABC transporters was aligned in 5 minutes and 24 GB of RAM.
 * Remarkable time and memory optimizations - SLINK has been replaced with Prim’s minimum spanning tree algorithm when constructing default (single linkage) guide trees. NOTE: This may change quality results slightly compared to FAMSA 1 due to different ties resolution.
 * Neighbour joining guide trees (`-gt nj` option). NOTE: Neighbour joining trees are calculated with a use of original *O*(*N*<sup>3</sup>) algorithm, thus their applicability on large sets is limited (unless they are used as subtrees with Medoid Tree heuristic), 
 * Option for compressing output aligment to gzip (`-gz` switch).
@@ -150,8 +150,8 @@ The analysis was performed on our extHomFam 2 benchmark produced by combining Ho
 | MAFFT PartTree  |  7.453 | `mafft --thread 32 --anysymbol --quiet --parttree <input> -o <output>` |
 | MAFFT DPPartTree  |  7.453 |  `mafft --thread 32 --anysymbol --quiet --dpparttree <input> -o <output>` |
 | FAMSA  | 1.6.2  | `famsa -t 32 <input> <output>`  |
-| FAMSA 2-rc | 2.0.0-rc  | `famsa -t 32 -gz <input> <output>`  |
-| FAMSA 2-rc Medoid | 2.0.0-rc  | `famsa -t 32 -medoidtree -gt upgma -gz <input> <output>`  |
+| FAMSA 2 | 2.0.1  | `famsa -t 32 -gz <input> <output>`  |
+| FAMSA 2 Medoid | 2.0.1  | `famsa -t 32 -medoidtree -gt upgma -gz <input> <output>`  |
 
 
 The tests were performed with 32 computing threads on a machine with AMD Ryzen Threadripper 3990X CPU and 256 GB of RAM. For each extHomFam 2 subset we measured a fraction of properly aligned columns (TC score) as well as a total running time and a maximum memory requirements. The results are presented in the figure below. Notches at boxplots indicate 95% confidence interval for median, triangle represent means. The missing series for some algorithm-set pairs indicate that either the algorithm failed to complete all the families in a set or the running times exceeded a week. FAMSA 2 alignments were stored in gzip format (`-gz` switch). 

makefile

@@ -11,9 +11,11 @@ UNAME_S := $(shell uname -s)
 ifeq ($(UNAME_S),Darwin)
 	GCC_VERSION=8
 	ABI_FLAG =
+	CLINK_FLAGS =
 else
 	GCC_VERSION = $(shell $(CXX) -dumpversion | cut -f1 -d.)
 	ABI_FLAG = -fabi-version=0 
+	CLINK_FLAGS = -lrt
 endif
 
 
@@ -100,16 +102,16 @@ endif
 
 
 ifeq ($(STATIC_LINK), true) 
-	CFLAGS	= -Wall -Wno-char-subscripts -Wno-attributes -O3 -$(COMMON_FLAGS) $(DEFINE_FLAGS) -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=$(CPP_STD) -I $(LIBS_DIR)
+	CXXFLAGS	= -Wall -Wno-char-subscripts -Wno-attributes -O3 -$(COMMON_FLAGS) $(DEFINE_FLAGS) -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=$(CPP_STD) -I $(LIBS_DIR)
 	CLINK	= -lm -static -O3 -msse4 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive -std=$(CPP_STD)
 else
-	CFLAGS	= -Wall -Wno-char-subscripts -Wno-attributes -O3 $(COMMON_FLAGS) $(DEFINE_FLAGS) -std=$(CPP_STD) -pthread -I $(LIBS_DIR)
-	CLINK	= -lm -O3 $(COMMON_FLAGS) -std=$(CPP_STD) -pthread 
+	CXXFLAGS	= -Wall -Wno-char-subscripts -Wno-attributes -O3 $(COMMON_FLAGS) $(DEFINE_FLAGS) -std=$(CPP_STD) -pthread -I $(LIBS_DIR)
+	CLINK	= -lm $(CLINK_FLAGS) -O3 $(COMMON_FLAGS) -std=$(CPP_STD) -pthread 
 endif
 
-CFLAGS_AVX = $(CFLAGS) -mavx ${ABI_FLAG} -mpopcnt -funroll-loops
-CFLAGS_AVX2 = $(CFLAGS) -mavx2 ${ABI_FLAG} -mpopcnt -funroll-loops
-CFLAGS_NEON = $(CFLAGS) ${ABI_FLAG} -funroll-loops
+CXXFLAGS_AVX = $(CXXFLAGS) -mavx ${ABI_FLAG} -mpopcnt -funroll-loops
+CXXFLAGS_AVX2 = $(CXXFLAGS) -mavx2 ${ABI_FLAG} -mpopcnt -funroll-loops
+CXXFLAGS_NEON = $(CXXFLAGS) ${ABI_FLAG} -funroll-loops
 
 
 
@@ -136,17 +138,17 @@ COMMON_OBJS := src/msa.o \
 	libs/mimalloc/static.o
 
 src/lcs/lcsbp_classic.o : src/lcs/lcsbp_classic.cpp
-	$(CXX) $(CFLAGS) -c src/lcs/lcsbp_classic.cpp -o $@
+	$(CXX) $(CXXFLAGS) -c src/lcs/lcsbp_classic.cpp -o $@
 
 ifeq ($(SIMD), NONE) 
 LCS_OBJS := src/lcs/lcsbp.o \
 	src/lcs/lcsbp_classic.o
 UTILS_OBJS := src/utils/utils.o 
 
 src/lcs/lcsbp.o : src/lcs/lcsbp.cpp
-	$(CXX) $(CFLAGS) -c src/lcs/lcsbp.cpp -o $@
+	$(CXX) $(CXXFLAGS) -c src/lcs/lcsbp.cpp -o $@
 src/utils/utils.o : src/utils/utils.cpp
-	$(CXX) $(CFLAGS) -c src/utils/utils.cpp -o $@
+	$(CXX) $(CXXFLAGS) -c src/utils/utils.cpp -o $@
 
 else ifeq ($(SIMD), AVX1)
 LCS_OBJS := src/lcs/lcsbp.o \
@@ -156,14 +158,14 @@ UTILS_OBJS := src/utils/utils.o \
 	src/utils/utils_avx.o 
 
 src/lcs/lcsbp.o : src/lcs/lcsbp.cpp
-	$(CXX) $(CFLAGS) -c src/lcs/lcsbp.cpp -o $@
+	$(CXX) $(CXXFLAGS) -c src/lcs/lcsbp.cpp -o $@
 src/lcs/lcsbp_avx_intr.o : src/lcs/lcsbp_avx_intr.cpp
-	$(CXX) $(CFLAGS_AVX) -c src/lcs/lcsbp_avx_intr.cpp -o $@
+	$(CXX) $(CXXFLAGS_AVX) -c src/lcs/lcsbp_avx_intr.cpp -o $@
 
 src/utils/utils.o : src/utils/utils.cpp
-	$(CXX) $(CFLAGS) -c src/utils/utils.cpp -o $@
+	$(CXX) $(CXXFLAGS) -c src/utils/utils.cpp -o $@
 src/utils/utils_avx.o : src/utils/utils_avx.cpp
-	$(CXX) $(CFLAGS_AVX) -c src/utils/utils_avx.cpp -o $@
+	$(CXX) $(CXXFLAGS_AVX) -c src/utils/utils_avx.cpp -o $@
 else ifeq ($(SIMD), NEON)
 LCS_OBJS := src/lcs/lcsbp.o \
 	src/lcs/lcsbp_classic.o \
@@ -172,14 +174,14 @@ UTILS_OBJS := src/utils/utils.o \
 	src/utils/utils_neon.o 
 
 src/lcs/lcsbp.o : src/lcs/lcsbp.cpp
-	$(CXX) $(CFLAGS) -c src/lcs/lcsbp.cpp -o $@
+	$(CXX) $(CXXFLAGS) -c src/lcs/lcsbp.cpp -o $@
 src/lcs/lcsbp_avx_intr.o : src/lcs/lcsbp_avx_intr.cpp
-	$(CXX) $(CFLAGS_NEON) -c src/lcs/lcsbp_neon_intr.cpp -o $@
+	$(CXX) $(CXXFLAGS_NEON) -c src/lcs/lcsbp_neon_intr.cpp -o $@
 
 src/utils/utils.o : src/utils/utils.cpp
-	$(CXX) $(CFLAGS) -c src/utils/utils.cpp -o $@
+	$(CXX) $(CXXFLAGS) -c src/utils/utils.cpp -o $@
 src/utils/utils_neon.o : src/utils/utils_neon.cpp
-	$(CXX) $(CFLAGS_NEON) -c src/utils/utils_neon.cpp -o $@
+	$(CXX) $(CXXFLAGS_NEON) -c src/utils/utils_neon.cpp -o $@
 else
 LCS_OBJS := src/lcs/lcsbp.o \
 	src/lcs/lcsbp_classic.o \
@@ -191,26 +193,23 @@ UTILS_OBJS := src/utils/utils.o \
 	src/utils/utils_avx2.o
 
 src/lcs/lcsbp.o : src/lcs/lcsbp.cpp
-	$(CXX) $(CFLAGS) -c src/lcs/lcsbp.cpp -o $@
+	$(CXX) $(CXXFLAGS) -c src/lcs/lcsbp.cpp -o $@
 src/lcs/lcsbp_avx_intr.o : src/lcs/lcsbp_avx_intr.cpp
-	$(CXX) $(CFLAGS_AVX) -c src/lcs/lcsbp_avx_intr.cpp -o $@
+	$(CXX) $(CXXFLAGS_AVX) -c src/lcs/lcsbp_avx_intr.cpp -o $@
 src/lcs/lcsbp_avx2_intr.o : src/lcs/lcsbp_avx2_intr.cpp
-	$(CXX) $(CFLAGS_AVX2) -c src/lcs/lcsbp_avx2_intr.cpp -o $@
+	$(CXX) $(CXXFLAGS_AVX2) -c src/lcs/lcsbp_avx2_intr.cpp -o $@
 
 src/utils/utils.o : src/utils/utils.cpp
-	$(CXX) $(CFLAGS) -c src/utils/utils.cpp -o $@
+	$(CXX) $(CXXFLAGS) -c src/utils/utils.cpp -o $@
 src/utils/utils_avx.o : src/utils/utils_avx.cpp
-	$(CXX) $(CFLAGS_AVX) -c src/utils/utils_avx.cpp -o $@
+	$(CXX) $(CXXFLAGS_AVX) -c src/utils/utils_avx.cpp -o $@
 src/utils/utils_avx2.o : src/utils/utils_avx2.cpp
-	$(CXX) $(CFLAGS_AVX2) -c src/utils/utils_avx2.cpp -o $@
+	$(CXX) $(CXXFLAGS_AVX2) -c src/utils/utils_avx2.cpp -o $@
 endif
 
 
 .cpp.o:
-	$(CXX) $(CFLAGS) -c $< -o $@
-
-.c.o:
-	$(CXX) $(CFLAGS) -c $< -o $@
+	$(CXX) $(CXXFLAGS) -c $< -o $@
 
 famsa: deflate src/famsa.o $(COMMON_OBJS) $(LCS_OBJS) $(UTILS_OBJS)
 	$(CXX) $(CLINK) -o $@ src/famsa.o $(COMMON_OBJS) $(LCS_OBJS) $(UTILS_OBJS) $(LIB_FILES)
@@ -222,6 +221,6 @@ clean:
 	-rm src/tree/*.o
 	-rm src/utils/*.o
 	-rm src/*.o
-	-rm lib/mimalloc/*.o
+	-rm libs/mimalloc/*.o
 	-rm famsa
 

src/core/version.h

@@ -9,18 +9,21 @@ Authors: Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Adam Gudys
 #ifndef _VERSION_H
 #define _VERSION_H
 
-#define FAMSA_VER		"2.0.0-rc"
-#define FAMSA_DATE		"2022-05-17"
+#define FAMSA_VER		"2.0.1"
+#define FAMSA_DATE		"2022-05-19"
 #define FAMSA_AUTHORS	"S. Deorowicz, A. Debudaj-Grabysz, A. Gudys"
 
 #endif
 
 /*
 Version history:
 
+2.0.1:
+- Several fixes for bioconda.
+
 2.0.0-rc:
-- default algorithm for single linkage trees changed from SLINK to MST Prim,
-- small fixes.
+- Default algorithm for single linkage trees changed from SLINK to MST Prim,
+- Small fixes.
 
 1.16.0 (2022-04-29):
  - mimalloc added as a single source library (no external linking).