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locks; strict;
comment	@# @;


1.2
date	2023.08.29.21.49.57;	author bacon;	state Exp;
branches;
next	1.1;
commitid	3t5B44MuRw1jiJCE;

1.1
date	2023.07.31.14.34.18;	author bacon;	state Exp;
branches;
next	;
commitid	qOkQl0Djtm2EOXyE;


desc
@@


1.2
log
@biology/rna-star: Fix build on Darwin 21.6.0 x86

Remove extern "C" in file build with c++
@
text
@$NetBSD$

# Portability

--- Makefile.orig	2022-11-01 14:50:35.000000000 +0000
+++ Makefile
@@@@ -11,6 +11,10 @@@@ CXXFLAGSextra ?=
 # user may define the compiler
 CXX ?= g++
 
+# user may set to '' and sed "htslib/htslib/*.h" to <htslib/*.h>
+# if they don't want the bundled htslib
+HTSLIB ?= htslib
+
 # pre-defined flags
 LDFLAGS_shared := -pthread -Lhtslib -Bstatic -lhts -Bdynamic -lz
 LDFLAGS_static := -static -static-libgcc -pthread -Lhtslib -lhts -lz
@@@@ -18,7 +22,8 @@@@ LDFLAGS_Mac :=-pthread -lz htslib/libhts
 LDFLAGS_Mac_static :=-pthread -lz -static-libgcc htslib/libhts.a
 LDFLAGS_gdb := $(LDFLAGS_shared)
 
-DATE_FMT = --iso-8601=seconds
+# --iso-8601 is not portable
+DATE_FMT = +%Y-%m-%dT%H:%M:%S%z
 ifdef SOURCE_DATE_EPOCH
     BUILD_DATE ?= $(shell date -u -d "@@$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u -r "$(SOURCE_DATE_EPOCH)" "$(DATE_FMT)" 2>/dev/null || date -u "$(DATE_FMT)")
 else
@@@@ -41,12 +46,12 @@@@ GIT_BRANCH_COMMIT_DIFF := -D'GIT_BRANCH_
 
 # Defaults, can be overridden by make arguments or environment
 CXXFLAGS ?= -pipe -Wall -Wextra
-CFLAGS ?= -pipe -Wall -Wextra -O3
+CFLAGS ?= -pipe -Wall -Wextra
 CXXFLAGS_SIMD ?= -mavx2
 
 # Unconditionally set essential flags and optimization options
 CXXFLAGS_common := -std=c++11 -fopenmp $(COMPTIMEPLACE) $(GIT_BRANCH_COMMIT_DIFF)
-CXXFLAGS_main := -O3 $(CXXFLAGS_common)
+CXXFLAGS_main := $(CXXFLAGS_common)
 CXXFLAGS_gdb := -O0 -g3 $(CXXFLAGS_common)
 
 ##########################################################################################################
@@@@ -114,7 +119,7 @@@@ clean:
 
 .PHONY: CLEAN
 CLEAN: clean
-	$(MAKE) -C htslib clean
+	$(MAKE) -C $(HTSLIB) clean
 
 
 .PHONY: clean_solo
@@@@ -131,10 +136,10 @@@@ ifneq ($(MAKECMDGOALS),CLEAN)
 ifneq ($(MAKECMDGOALS),clean_solo)
 ifneq ($(MAKECMDGOALS),STARforMac)
 ifneq ($(MAKECMDGOALS),STARforMacGDB)
-Depend.list: $(SOURCES) parametersDefault.xxd htslib
+Depend.list: $(SOURCES) parametersDefault.xxd $(HTSLIB)
 	echo $(SOURCES)
 	'rm' -f ./Depend.list
-	$(CXX) $(CXXFLAGS_common) -MM $^ >> Depend.list
+	$(CXX) $(CXXFLAGS) $(CXXFLAGS_common) -MM $^ >> Depend.list
 include Depend.list
 endif
 endif
@


1.1
log
@biology/rna-star: Spliced Transcripts Align to a Ref

STAR (Spliced Transcripts Alignment to a Reference) aims to achieve
accurate alignment of high-throughput RNA-seq data.  STAR is based on
a previously undescribed RNA-seq alignment algorithm that uses
sequential maximum mappable seed search in uncompressed suffix arrays
followed by seed clustering and stitching procedure. STAR outperforms
other aligners by a factor of >50 in mapping speed, aligning to the
human genome 550 million 2 x 76 bp paired-end reads per hour on a modest
12-core server, while at the same time improving alignment sensitivity
and precision.
@
text
@@