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head/biology/samtools/files/patch-Makefile
| --- Makefile.orig 2016-04-22 09:22:44 UTC | --- Makefile.orig 2017-09-28 11:12:01 UTC | ||||
| +++ Makefile | +++ Makefile | ||||
| @@ -38,18 +38,18 @@ AOBJS= bam_index.o bam_plcmd.o sam_ | @@ -40,23 +40,22 @@ AOBJS= bam_index.o bam_plcmd.o sam_ | ||||
| bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ | bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \ | ||||
| bam_quickcheck.o bam_addrprg.o | bam_quickcheck.o bam_addrprg.o bam_markdup.o | ||||
| -prefix = /usr/local | -prefix = /usr/local | ||||
| +prefix = ${STAGEDIR}${PREFIX} | +prefix = ${PREFIX} | ||||
| exec_prefix = $(prefix) | exec_prefix = $(prefix) | ||||
| bindir = $(exec_prefix)/bin | bindir = $(exec_prefix)/bin | ||||
| datarootdir = $(prefix)/share | datarootdir = $(prefix)/share | ||||
| -mandir = $(datarootdir)/man | -mandir = $(datarootdir)/man | ||||
| +mandir = $(prefix)/man | +mandir = $(prefix)/man | ||||
| man1dir = $(mandir)/man1 | man1dir = $(mandir)/man1 | ||||
| -MKDIR_P = mkdir -p | # Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS) | ||||
| -misc_bindir = $(bindir) | |||||
| +misc_bindir = $(bindir)/samtools_misc | |||||
| MKDIR_P = mkdir -p | |||||
| -INSTALL = install -p | -INSTALL = install -p | ||||
| -INSTALL_PROGRAM = $(INSTALL) | |||||
| -INSTALL_DATA = $(INSTALL) -m 644 | -INSTALL_DATA = $(INSTALL) -m 644 | ||||
| -INSTALL_DIR = $(MKDIR_P) -m 755 | -INSTALL_DIR = $(MKDIR_P) -m 755 | ||||
| +#MKDIR_P = mkdir -p | -INSTALL_MAN = $(INSTALL_DATA) | ||||
| +#INSTALL = install -p | -INSTALL_PROGRAM = $(INSTALL) | ||||
| +#INSTALL_PROGRAM = $(INSTALL) | -INSTALL_SCRIPT = $(INSTALL_PROGRAM) | ||||
| +#INSTALL_DATA = $(INSTALL) -m 644 | +INSTALL_DATA = ${BSD_INSTALL_DATA} | ||||
| +#INSTALL_DIR = $(MKDIR_P) -m 755 | +INSTALL_DIR = $(MKDIR_P) | ||||
| +INSTALL_MAN = ${BSD_INSTALL_MAN} | |||||
| +INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM} | |||||
| +INSTALL_SCRIPT = ${BSD_INSTALL_SCRIPT} | |||||
| PROGRAMS = samtools | PROGRAMS = samtools | ||||
| @@ -59,7 +59,6 @@ BUILT_MISC_PROGRAMS = \ | |||||
| misc/md5fa misc/md5sum-lite misc/wgsim | |||||
| MISC_PROGRAMS = \ | |||||
| - $(BUILT_MISC_PROGRAMS) \ | |||||
| misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \ | |||||
| misc/interpolate_sam.pl misc/novo2sam.pl \ | |||||
| misc/plot-bamstats misc/psl2sam.pl \ | |||||
| @@ -82,7 +81,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) | |||||
| # TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally | |||||
| ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS) | |||||
| ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS) | |||||
| -ALL_LIBS = -lz -ldl $(LIBS) | |||||
| +ALL_LIBS = -lz $(LIBS) | |||||
| # Usually config.mk and config.h are generated by running configure | |||||
| # or config.status, but if those aren't used create defaults here. | |||||
| @@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c conf | |||||
| install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) | |||||
| - $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) | |||||
| - $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir) | |||||
| + $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir) | |||||
| + $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir) | |||||
| + $(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc | |||||
| + $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc | |||||
| $(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir) | |||||