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04b3bb054f
Changes: https://sourceforge.net/p/samtools/mailman/message/35033807/ PR: 209653 Submitted by: cartwright@asu.edu (maintainer)
58 lines
2.1 KiB
Text
58 lines
2.1 KiB
Text
--- Makefile.orig 2016-04-22 09:22:44 UTC
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+++ Makefile
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@@ -38,18 +38,18 @@ AOBJS= bam_index.o bam_plcmd.o sam_
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bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
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bam_quickcheck.o bam_addrprg.o
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-prefix = /usr/local
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+prefix = ${STAGEDIR}${PREFIX}
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exec_prefix = $(prefix)
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bindir = $(exec_prefix)/bin
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datarootdir = $(prefix)/share
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-mandir = $(datarootdir)/man
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+mandir = $(prefix)/man
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man1dir = $(mandir)/man1
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-MKDIR_P = mkdir -p
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-INSTALL = install -p
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-INSTALL_PROGRAM = $(INSTALL)
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-INSTALL_DATA = $(INSTALL) -m 644
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-INSTALL_DIR = $(MKDIR_P) -m 755
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+#MKDIR_P = mkdir -p
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+#INSTALL = install -p
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+#INSTALL_PROGRAM = $(INSTALL)
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+#INSTALL_DATA = $(INSTALL) -m 644
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+#INSTALL_DIR = $(MKDIR_P) -m 755
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PROGRAMS = samtools
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@@ -59,7 +59,6 @@ BUILT_MISC_PROGRAMS = \
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misc/md5fa misc/md5sum-lite misc/wgsim
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MISC_PROGRAMS = \
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- $(BUILT_MISC_PROGRAMS) \
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misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
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misc/interpolate_sam.pl misc/novo2sam.pl \
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misc/plot-bamstats misc/psl2sam.pl \
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@@ -82,7 +81,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
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# TODO Use configure or htslib.pc to add -rdynamic/-ldl conditionally
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ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
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ALL_LDFLAGS = -rdynamic $(HTSLIB_LDFLAGS) $(LDFLAGS)
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-ALL_LIBS = -lz -ldl $(LIBS)
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+ALL_LIBS = -lz $(LIBS)
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# Usually config.mk and config.h are generated by running configure
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# or config.status, but if those aren't used create defaults here.
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@@ -280,8 +279,10 @@ misc/maq2sam-long.o: misc/maq2sam.c conf
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install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
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- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
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- $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
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+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir)
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+ $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
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+ $(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
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+ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
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$(INSTALL_DATA) samtools.1 misc/wgsim.1 $(DESTDIR)$(man1dir)
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