STAR compile by cygwin error

[yjjeong86]

Hello Alex,

I was able to install the STAR on my Mac but it has low memory, so I am trying to install the STAR on the lab desktop (Windows10). I've used cygwin to build gcc and trying to compile the STAR but it gives the following error message and I am lost now.

g++ -c -O3 -std=c++11 -fopenmp -D'COMPILATION_TIME_PLACE="2021-12-21T12:51:40-06:00 DESKTOP-DL9FPKG:/home/dongsu/STAR-2.7.9a/source"' -pipe -Wall -Wextra SoloFeature_outputResults.cpp
SoloFeature_outputResults.cpp: In member function ‘void SoloFeature::outputResults(bool, std::string)’:
SoloFeature_outputResults.cpp:41:13: error: ‘symlink’ was not declared in this scope
41 | symlink("../../../SJ.out.tab", (outputPrefixMat+pSolo.outFileNames[1]).c_str());
| ^~~~~~~
make: *** [Makefile:88: SoloFeature_outputResults.o] Error 1

gcc information is as below

$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-cygwin/11/lto-wrapper.exe
Target: x86_64-pc-cygwin
Configured with: /mnt/share/cygpkgs/gcc/gcc.x86_64/src/gcc-11.2.0/configure --srcdir=/mnt/share/cygpkgs/gcc/gcc.x86_64/src/gcc-11.2.0 --prefix=/usr --exec-prefix=/usr --localstatedir=/var --sysconfdir=/etc --docdir=/usr/share/doc/gcc --htmldir=/usr/share/doc/gcc/html -C --build=x86_64-pc-cygwin --host=x86_64-pc-cygwin --target=x86_64-pc-cygwin --without-libiconv-prefix --without-libintl-prefix --libexecdir=/usr/lib --with-gcc-major-version-only --enable-shared --enable-shared-libgcc --enable-static --enable-version-specific-runtime-libs --enable-bootstrap --enable-__cxa_atexit --with-dwarf2 --with-tune=generic --disable-bootstrap --enable-languages=c,c++,fortran,lto,objc,obj-c++,jit --enable-graphite --enable-threads=posix --enable-libatomic --enable-libgomp --enable-libquadmath --enable-libquadmath-support --disable-libssp --enable-libada --disable-symvers --with-gnu-ld --with-gnu-as --with-cloog-include=/usr/include/cloog-isl --without-libiconv-prefix --without-libintl-prefix --with-system-zlib --enable-linker-build-id --with-default-libstdcxx-abi=gcc4-compatible --enable-libstdcxx-filesystem-ts
Thread model: posix
Supported LTO compression algorithms: zlib zstd
gcc version 11.2.0 (GCC)

I am really new to the bioinformatics so please bear with me if I made a simple mistake or not understanding well.

Help will be appreciated!

Jae

[alexdobin]

Hi Jae,

STAR code uses a number of Linux-specific commands (symlink is one example) and cannot be compiled under Windows.
You can try to run it under WSL, though users reported troubles with it.
The best option is to add the dual-boot to your desktop to run a full-fledged Linux.

Cheers
Alex