質問編集履歴
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ちなみに Makefile の中身はこんな感じです。
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```makefile
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CC= gcc
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CFLAGS= -g -Wall -O2
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#LDFLAGS= -Wl,-rpath,$$ORIGIN/../lib
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DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
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KNETFILE_O= knetfile.o
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LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
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bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
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$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
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AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
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bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
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bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
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cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \
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bam_tview_curses.o bam_tview_html.o
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PROG= samtools
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INCLUDES= -I.
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SUBDIRS= . bcftools misc
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LIBPATH=
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LIBCURSES= -lcurses # -lXCurses
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.SUFFIXES:.c .o
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.PHONY: all lib
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.c.o:
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$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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all-recur lib-recur clean-recur cleanlocal-recur install-recur:
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@target=`echo $@ | sed s/-recur//`; \
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wdir=`pwd`; \
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list='$(SUBDIRS)'; for subdir in $$list; do \
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cd $$subdir; \
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$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
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cd $$wdir; \
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done;
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all:$(PROG)
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.PHONY:all lib clean cleanlocal
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.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
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lib:libbam.a
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libbam.a:$(LOBJS)
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$(AR) -csru $@ $(LOBJS)
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samtools:lib-recur $(AOBJS)
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$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
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razip:razip.o razf.o $(KNETFILE_O)
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$(CC) $(CFLAGS) -o $@ $^ -lz
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bgzip:bgzip.o bgzf.o $(KNETFILE_O)
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$(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
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bgzf.o:bgzf.c bgzf.h
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$(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
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razip.o:razf.h
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bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
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sam.o:sam.h bam.h
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bam_import.o:bam.h kseq.h khash.h razf.h
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bam_pileup.o:bam.h razf.h ksort.h
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bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
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bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
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bam_lpileup.o:bam.h ksort.h
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bam_tview.o:bam.h faidx.h bam_tview.h
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bam_tview_curses.o:bam.h faidx.h bam_tview.h
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bam_tview_html.o:bam.h faidx.h bam_tview.h
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bam_sort.o:bam.h ksort.h razf.h
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bam_md.o:bam.h faidx.h
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sam_header.o:sam_header.h khash.h
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bcf.o:bcftools/bcf.h
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bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
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bam2bcf_indel.o:bam2bcf.h
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errmod.o:errmod.h
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phase.o:bam.h khash.h ksort.h
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bamtk.o:bam.h
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faidx.o:faidx.h razf.h khash.h
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faidx_main.o:faidx.h razf.h
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libbam.1.dylib-local:$(LOBJS)
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libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
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libbam.so.1-local:$(LOBJS)
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$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
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dylib:
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@$(MAKE) cleanlocal; \
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case `uname` in \
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Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
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Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
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*) echo 'Unknown OS';; \
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esac
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cleanlocal:
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rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
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clean:cleanlocal-recur
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$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
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libbam.1.dylib-local:$(LOBJS)
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libbam.so.1-local:$(LOBJS)
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dylib:
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*) echo 'Unknown OS';; \
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cleanlocal:
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clean:cleanlocal-recur
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+
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もう一つは、ややこしくどこから見ていけばいいのかもわかりません...
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```makefile
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all:
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cd lib && ${MAKE}
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cd jkOwnLib && ${MAKE}
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+
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cd blat && $(MAKE)
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|
+
|
|
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|
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cd gfClient && $(MAKE)
|
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|
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|
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257
|
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cd gfServer && $(MAKE)
|
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|
+
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|
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|
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cd hg/pslPretty && $(MAKE)
|
|
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+
|
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261
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+
cd hg/pslReps && $(MAKE)
|
|
262
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+
|
|
263
|
+
cd hg/pslSort && $(MAKE)
|
|
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|
+
|
|
265
|
+
cd utils/nibFrag && $(MAKE)
|
|
266
|
+
|
|
267
|
+
cd utils/faToNib && $(MAKE)
|
|
268
|
+
|
|
269
|
+
cd utils/faToTwoBit && $(MAKE)
|
|
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|
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271
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+
cd utils/twoBitToFa && $(MAKE)
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|
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273
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cd utils/twoBitInfo && $(MAKE)
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|
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cd webBlat && $(MAKE)
|
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clean:
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rm -f */*.o */*/*.o lib/*/*.a
|
|
236
282
|
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237
283
|
```
|
|
238
|
-
|
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239
|
-
|
|
240
|
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|
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|
|
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|
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|
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|
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all:
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|
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|
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|
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cd lib && ${MAKE}
|
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|
-
|
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|
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cd jkOwnLib && ${MAKE}
|
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|
-
|
|
253
|
-
cd blat && $(MAKE)
|
|
254
|
-
|
|
255
|
-
cd gfClient && $(MAKE)
|
|
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|
-
|
|
257
|
-
cd gfServer && $(MAKE)
|
|
258
|
-
|
|
259
|
-
cd hg/pslPretty && $(MAKE)
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|
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|
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cd hg/pslReps && $(MAKE)
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|
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|
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|
|
263
|
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|
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|
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|
|
265
|
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cd utils/nibFrag && $(MAKE)
|
|
266
|
-
|
|
267
|
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cd utils/faToNib && $(MAKE)
|
|
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|
-
|
|
269
|
-
cd utils/faToTwoBit && $(MAKE)
|
|
270
|
-
|
|
271
|
-
cd utils/twoBitToFa && $(MAKE)
|
|
272
|
-
|
|
273
|
-
cd utils/twoBitInfo && $(MAKE)
|
|
274
|
-
|
|
275
|
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cd webBlat && $(MAKE)
|
|
276
|
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|
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|
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|
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rm -f */*.o */*/*.o lib/*/*.a
|
|
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|
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|
|
283
|
-
```
|
3
makefile の中身追加
test
CHANGED
|
File without changes
|
test
CHANGED
|
@@ -25,3 +25,259 @@
|
|
|
25
25
|
ググっても欲しい情報がなかなか手に入らず、困っています。
|
|
26
26
|
|
|
27
27
|
初歩的な質問でお恥ずかしいのですが、ご回答いただけたら幸いです。
|
|
28
|
+
|
|
29
|
+
|
|
30
|
+
|
|
31
|
+
ちなみに Makefile の中身はこんな感じです。
|
|
32
|
+
|
|
33
|
+
```
|
|
34
|
+
|
|
35
|
+
CC= gcc
|
|
36
|
+
|
|
37
|
+
CFLAGS= -g -Wall -O2
|
|
38
|
+
|
|
39
|
+
#LDFLAGS= -Wl,-rpath,$$ORIGIN/../lib
|
|
40
|
+
|
|
41
|
+
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
|
|
42
|
+
|
|
43
|
+
KNETFILE_O= knetfile.o
|
|
44
|
+
|
|
45
|
+
LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
|
|
46
|
+
|
|
47
|
+
bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
|
|
48
|
+
|
|
49
|
+
$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
|
|
50
|
+
|
|
51
|
+
AOBJS= bam_tview.o bam_plcmd.o sam_view.o \
|
|
52
|
+
|
|
53
|
+
bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
|
|
54
|
+
|
|
55
|
+
bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
|
|
56
|
+
|
|
57
|
+
cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \
|
|
58
|
+
|
|
59
|
+
bam_tview_curses.o bam_tview_html.o
|
|
60
|
+
|
|
61
|
+
PROG= samtools
|
|
62
|
+
|
|
63
|
+
INCLUDES= -I.
|
|
64
|
+
|
|
65
|
+
SUBDIRS= . bcftools misc
|
|
66
|
+
|
|
67
|
+
LIBPATH=
|
|
68
|
+
|
|
69
|
+
LIBCURSES= -lcurses # -lXCurses
|
|
70
|
+
|
|
71
|
+
|
|
72
|
+
|
|
73
|
+
.SUFFIXES:.c .o
|
|
74
|
+
|
|
75
|
+
.PHONY: all lib
|
|
76
|
+
|
|
77
|
+
|
|
78
|
+
|
|
79
|
+
.c.o:
|
|
80
|
+
|
|
81
|
+
$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
|
|
82
|
+
|
|
83
|
+
|
|
84
|
+
|
|
85
|
+
all-recur lib-recur clean-recur cleanlocal-recur install-recur:
|
|
86
|
+
|
|
87
|
+
@target=`echo $@ | sed s/-recur//`; \
|
|
88
|
+
|
|
89
|
+
wdir=`pwd`; \
|
|
90
|
+
|
|
91
|
+
list='$(SUBDIRS)'; for subdir in $$list; do \
|
|
92
|
+
|
|
93
|
+
cd $$subdir; \
|
|
94
|
+
|
|
95
|
+
$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
|
|
96
|
+
|
|
97
|
+
INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
|
|
98
|
+
|
|
99
|
+
cd $$wdir; \
|
|
100
|
+
|
|
101
|
+
done;
|
|
102
|
+
|
|
103
|
+
|
|
104
|
+
|
|
105
|
+
all:$(PROG)
|
|
106
|
+
|
|
107
|
+
|
|
108
|
+
|
|
109
|
+
.PHONY:all lib clean cleanlocal
|
|
110
|
+
|
|
111
|
+
.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
|
|
112
|
+
|
|
113
|
+
|
|
114
|
+
|
|
115
|
+
lib:libbam.a
|
|
116
|
+
|
|
117
|
+
|
|
118
|
+
|
|
119
|
+
libbam.a:$(LOBJS)
|
|
120
|
+
|
|
121
|
+
$(AR) -csru $@ $(LOBJS)
|
|
122
|
+
|
|
123
|
+
|
|
124
|
+
|
|
125
|
+
samtools:lib-recur $(AOBJS)
|
|
126
|
+
|
|
127
|
+
$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
|
|
128
|
+
|
|
129
|
+
|
|
130
|
+
|
|
131
|
+
razip:razip.o razf.o $(KNETFILE_O)
|
|
132
|
+
|
|
133
|
+
$(CC) $(CFLAGS) -o $@ $^ -lz
|
|
134
|
+
|
|
135
|
+
|
|
136
|
+
|
|
137
|
+
bgzip:bgzip.o bgzf.o $(KNETFILE_O)
|
|
138
|
+
|
|
139
|
+
$(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
|
|
140
|
+
|
|
141
|
+
|
|
142
|
+
|
|
143
|
+
bgzf.o:bgzf.c bgzf.h
|
|
144
|
+
|
|
145
|
+
$(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
|
|
146
|
+
|
|
147
|
+
|
|
148
|
+
|
|
149
|
+
razip.o:razf.h
|
|
150
|
+
|
|
151
|
+
bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
|
|
152
|
+
|
|
153
|
+
sam.o:sam.h bam.h
|
|
154
|
+
|
|
155
|
+
bam_import.o:bam.h kseq.h khash.h razf.h
|
|
156
|
+
|
|
157
|
+
bam_pileup.o:bam.h razf.h ksort.h
|
|
158
|
+
|
|
159
|
+
bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
|
|
160
|
+
|
|
161
|
+
bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
|
|
162
|
+
|
|
163
|
+
bam_lpileup.o:bam.h ksort.h
|
|
164
|
+
|
|
165
|
+
bam_tview.o:bam.h faidx.h bam_tview.h
|
|
166
|
+
|
|
167
|
+
bam_tview_curses.o:bam.h faidx.h bam_tview.h
|
|
168
|
+
|
|
169
|
+
bam_tview_html.o:bam.h faidx.h bam_tview.h
|
|
170
|
+
|
|
171
|
+
bam_sort.o:bam.h ksort.h razf.h
|
|
172
|
+
|
|
173
|
+
bam_md.o:bam.h faidx.h
|
|
174
|
+
|
|
175
|
+
sam_header.o:sam_header.h khash.h
|
|
176
|
+
|
|
177
|
+
bcf.o:bcftools/bcf.h
|
|
178
|
+
|
|
179
|
+
bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
|
|
180
|
+
|
|
181
|
+
bam2bcf_indel.o:bam2bcf.h
|
|
182
|
+
|
|
183
|
+
errmod.o:errmod.h
|
|
184
|
+
|
|
185
|
+
phase.o:bam.h khash.h ksort.h
|
|
186
|
+
|
|
187
|
+
bamtk.o:bam.h
|
|
188
|
+
|
|
189
|
+
|
|
190
|
+
|
|
191
|
+
faidx.o:faidx.h razf.h khash.h
|
|
192
|
+
|
|
193
|
+
faidx_main.o:faidx.h razf.h
|
|
194
|
+
|
|
195
|
+
|
|
196
|
+
|
|
197
|
+
|
|
198
|
+
|
|
199
|
+
libbam.1.dylib-local:$(LOBJS)
|
|
200
|
+
|
|
201
|
+
libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
|
|
202
|
+
|
|
203
|
+
|
|
204
|
+
|
|
205
|
+
libbam.so.1-local:$(LOBJS)
|
|
206
|
+
|
|
207
|
+
$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
|
|
208
|
+
|
|
209
|
+
|
|
210
|
+
|
|
211
|
+
dylib:
|
|
212
|
+
|
|
213
|
+
@$(MAKE) cleanlocal; \
|
|
214
|
+
|
|
215
|
+
case `uname` in \
|
|
216
|
+
|
|
217
|
+
Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
|
|
218
|
+
|
|
219
|
+
Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
|
|
220
|
+
|
|
221
|
+
*) echo 'Unknown OS';; \
|
|
222
|
+
|
|
223
|
+
esac
|
|
224
|
+
|
|
225
|
+
|
|
226
|
+
|
|
227
|
+
|
|
228
|
+
|
|
229
|
+
cleanlocal:
|
|
230
|
+
|
|
231
|
+
rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
|
|
232
|
+
|
|
233
|
+
|
|
234
|
+
|
|
235
|
+
clean:cleanlocal-recur
|
|
236
|
+
|
|
237
|
+
```
|
|
238
|
+
|
|
239
|
+
|
|
240
|
+
|
|
241
|
+
もう一つは、ややこしくどこから見ていけばいいのかもわかりません...
|
|
242
|
+
|
|
243
|
+
```
|
|
244
|
+
|
|
245
|
+
|
|
246
|
+
|
|
247
|
+
all:
|
|
248
|
+
|
|
249
|
+
cd lib && ${MAKE}
|
|
250
|
+
|
|
251
|
+
cd jkOwnLib && ${MAKE}
|
|
252
|
+
|
|
253
|
+
cd blat && $(MAKE)
|
|
254
|
+
|
|
255
|
+
cd gfClient && $(MAKE)
|
|
256
|
+
|
|
257
|
+
cd gfServer && $(MAKE)
|
|
258
|
+
|
|
259
|
+
cd hg/pslPretty && $(MAKE)
|
|
260
|
+
|
|
261
|
+
cd hg/pslReps && $(MAKE)
|
|
262
|
+
|
|
263
|
+
cd hg/pslSort && $(MAKE)
|
|
264
|
+
|
|
265
|
+
cd utils/nibFrag && $(MAKE)
|
|
266
|
+
|
|
267
|
+
cd utils/faToNib && $(MAKE)
|
|
268
|
+
|
|
269
|
+
cd utils/faToTwoBit && $(MAKE)
|
|
270
|
+
|
|
271
|
+
cd utils/twoBitToFa && $(MAKE)
|
|
272
|
+
|
|
273
|
+
cd utils/twoBitInfo && $(MAKE)
|
|
274
|
+
|
|
275
|
+
cd webBlat && $(MAKE)
|
|
276
|
+
|
|
277
|
+
|
|
278
|
+
|
|
279
|
+
clean:
|
|
280
|
+
|
|
281
|
+
rm -f */*.o */*/*.o lib/*/*.a
|
|
282
|
+
|
|
283
|
+
```
|
2
追加
test
CHANGED
|
File without changes
|
test
CHANGED
|
@@ -16,6 +16,8 @@
|
|
|
16
16
|
|
|
17
17
|
|
|
18
18
|
|
|
19
|
+
インストールしたいものの中に configure がなく、makefile の
|
|
20
|
+
|
|
19
21
|
どこかに PREFIX や BINDIR があるのではと探してはいるもののやはり、よくわかりません。
|
|
20
22
|
|
|
21
23
|
|
1
誤字
test
CHANGED
|
File without changes
|
test
CHANGED
|
@@ -20,4 +20,6 @@
|
|
|
20
20
|
|
|
21
21
|
|
|
22
22
|
|
|
23
|
+
ググっても欲しい情報がなかなか手に入らず、困っています。
|
|
24
|
+
|
|
23
25
|
初歩的な質問でお恥ずかしいのですが、ご回答いただけたら幸いです。
|