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I'm trying to install samtools () on cygwin. I followed the various tricks here and here but looks like my problem is that i can't have a functioning pthread. gcc is installed and works, zlib is installed and works and ncurses is installed and works + everything was added to the $PATH...but when i run make and it gets to the following line in Makefile:

gcc -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz

then it throws an error because it doesn't recognize the unix command -pthread. now...pthread should be a part of the default installation in cygwin so I don't understand why this is not working...

any hint would be great!

alk
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TriRook
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1 Answers1

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gcc's option -pthread is not available on Cygwin.

alk
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