Thursday, 11 September 2014

SAMtools 1.0 under Cygwin 64 bit Win7

 I successfully compiled SAMtools 1.0 under Cygwin using this instructions.
The standard Cygwin 64 bit installation I upgraded with:
nano,  gcc-core, make, git, libncurses-devel
I used the package from here and decompressed it with "bzip2 -d" and untarred it with "tar -vxf".
In ".bash_profile" I extended the PATH by adding "export PATH=/bin:$PATH".
I edited the beginning of the Makefile, but not the Makefile.mingw, as described in the post, using
CC       = gcc
CPPFLAGS = $(DFLAGS) $(INCLUDES)
CFLAGS   = -g -Wall -O2
CFLAGS   =-I/usr/include/ncurses
LDFLAGS  =
LDLIBS   =
DFLAGS=     -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -D_USE_KNETFILE
KNETFILE_O= knetfile.o
Than just "make" and "make install" and samtools ended up in /usr/local/bin

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