I have looked for hours and cannot seem to find an answer to my issue. I have installed zlib using the sources from zlib.net with mingw32-make -fwin32/Makefile.gcc && mingw32-make install -fwin32/Makefile.gcc like it says in the the Makefile.gcc file as well as trying to install via mingw-get install zlib and mingw-get install zlib-dev and the correct files get into the compile folders:
cp -fp zlib.h '/mingw/include'
cp -fp zconf.h '/mingw/include'
cp -fp libz.a '/mingw/lib'
But then I try to compile RSEM version 1.3.1 via mingw32-make and for some reason mingw cannot find the zlib.h file when it is literally in the C:\MinGW\include folder. Where can I can my MinGW build machine path?
Here are my results:
RSEM-1.3.1$ mingw32-make
g++ -o rsem-extract-reference-transcripts extractRef.o
g++ -o rsem-synthesis-reference-transcripts synthesisRef.o
g++ -o rsem-preref preRef.o
g++ -o rsem-build-read-index buildReadIndex.o
g++ -o rsem-simulate-reads simulation.o
cd samtools-1.3 && ./configure --without-curses && C:/Perl64/site/lib/auto/MinGW/bin/mingw32-make -f Makefile samtools
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.exe
checking for suffix of executables... .exe
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking location of HTSlib source tree... htslib-1.3
checking for zlib.h... no
checking for inflate in -lz... no
configure: error: zlib development files not found
Samtools uses compression routines from the zlib library <http://zlib.net>.
Building samtools requires zlib development files to be installed on the build
machine; you may need to ensure a package such as zlib1g-dev (on Debian or
Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed.
FAILED. This error must be resolved in order to build samtools successfully.
./configure: line 38: sort: No such file or directory
./configure: line 35: sed: No such file or directory
mingw32-make: *** [samtools-1.3/samtools] Error 1
