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From: "Buchbinder, Barry (NIH/NIAID) [E]" <BBuchbinder AT niaid DOT nih DOT gov>
To: "cygwin AT cygwin DOT com" <cygwin AT cygwin DOT com>
CC: "'De-Jian Zhao'" <dejian DOT zhao AT gmail DOT com>
Date: Wed, 18 Apr 2012 19:09:16 -0400
Subject: RE: Can RPM packages be installed into Cygwin?
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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.