De-Jian, Hello. It's me again.
I suspect that just writing wrapper scripts would be faster than playing with RPMs and/or trying to compile blast yourself. As I understand it, blast programs are all command-line. I think that the easiest thing would be to just use the Windows version supplied by NCBI and write wrapper scripts that will convert cygwin's POSIX paths to Windows paths. You might have to experiment to see if you also need to convert file formats from \n to \r\n line endings. See $ man cygpath $ man dos2unix $ man unix2dos Luc Hermitte's cyg-wrapper.sh might be all you need. http://hermitte.free.fr/cygwin/#Win32 Example (using vim): http://vim.wikia.com/wiki/Running_the_win32-version_of_Vim_from_cygwin I've never used cyg-wrapper.sh, so this suggestion is "theoretical" and not based on my personal experience. Related: http://www.ncbi.nlm.nih.gov/books/NBK1762/ http://www.ncbi.nlm.nih.gov/books/NBK52637/ Good luck, - Barry Disclaimer: Statements made herein are not made on behalf of NIAID. Disclaimer: Please see http://cygwin.com/ml/cygwin/2012-04/msg00247.html for other disclaimers and statements concerning the limited reliability of my advice on this topic.
