I think I have found out the problem, but don;t know how to solve it.
Samtools in cygwim
./configure and make show no visible error when run
however. nots by me below [[...]]
$ make install
mkdir -p -m 755 /usr/local/bin /usr/local/share/man/man1 [[the things in this
folder are htsfile.1and tabix.1]]
install -p samtools misc/ace2sam misc/maq2sam-long misc/maq2sam-short
misc/md5fa misc/md5sum-lite misc/wgsim misc/blast2sam.pl misc/bowtie2sam.pl
misc/export2sam.pl misc/interpolate_sam.pl misc/novo2sam.pl misc/plot-bamstats
misc/psl2sam.pl misc/sam2vcf.pl misc/samtools.pl misc/seq_cache_populate.pl
misc/soap2sam.pl misc/varfilter.py misc/wgsim_eval.pl misc/zoom2sam.pl
/usr/local/bin
install: omitting directory ‘samtools’his [[Already exists in /bin
/samtools-3.1]]
Makefile:290: recipe for target 'install' failed
make: *** [install] Error 1
The only file I cannot find in /bin is samtools application whereas the
applications from htslib and samtools-1.3/misc are all there
Gives this!
I believe the following are the relevant sections from makefile
52 MKDIR_P = mkdir -p
53 INSTALL = install -p
54 INSTALL_PROGRAM = $(INSTALL)
55 INSTALL_DATA = $(INSTALL) -m 644
56 INSTALL_DIR = $(MKDIR_P) -m 755
59 PROGRAMS = samtools
60 samtools = samtools-3.1/samtools
61 ##added 60
62 BUILT_MISC_PROGRAMS = \
63 misc/ace2sam misc/maq2sam-long misc/maq2sam-short \
64 misc/md5fa misc/md5sum-lite misc/wgsim
85 all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS)
143 ##samtools removed and replaced with (PROGRAMS)
144 (PROGRAMS): $(AOBJS) libbam.a $(HTSLIB)
145 $(CC) -pthread $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB_LIB)
$(CURSES_LIB) -lm $(ALL_LIBS)
289 install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
290 $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
291 $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
292 $(INSTALL_DATA) $(PROGRAMS) misc/wgsim.1 $(DESTDIR)$(man1dir)
from what I figure it does not know where samtools application is. It is in the
Samtools-1.3 folder.
anyone help with the correct command/words and where yhey should be placed.
Bob May
DNA Projects I2b L415, I2c L596 HG, Spriggs of Cleve SA Family & Tyler Surname
and ISOGG YTree
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