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alexdobin / STAR

RNA-seq aligner
MIT License
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STAR installation in cygwin #544

Open oyoki opened 5 years ago

oyoki commented 5 years ago

Hi Alex,

I have been trying to install STAR on cygwin and have resolved the other reported installation issues based on previous comments (modification of SharedMemory.cpp and Parameters_openReadsFiles.cpp). Those fixes resolved the other issues but I'm still getting this error when I try to compile

$ g++ STAR.cpp -o STAR STAR.cpp: In function ‘void usage()’: STAR.cpp:40:18: error: ‘parametersDefault’ was not declared in this scope std::cout << parametersDefault; ^~~~~ STAR.cpp:40:18: note: suggested alternative: ‘ParametersGenome’ std::cout << parametersDefault; ^~~~~ ParametersGenome

I've also used the 'make' and 'gcc' commands and I get the same error. Any assistance you can give would be very much appreciated. Thanks.

Best, Oyinda

alexdobin commented 5 years ago

Hi Oyinda,

I think something is wrong with the parametersDeafult.xxd file. Please try to copy it directly from the STAR distribution.

If you could make STAR work In Windows under cygwin, and share the results with the community, it would be great!

Cheers Alex