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Date:	Thu, 19 Apr 2012 15:23:19 +0800
From:	De-Jian Zhao <dejian DOT zhao AT gmail DOT com>
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To:	"Buchbinder, Barry (NIH/NIAID) [E]" <BBuchbinder AT niaid DOT nih DOT gov>
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Subject:	Re: Can RPM packages be installed into Cygwin?
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On 2012-4-19 7:09, Buchbinder, Barry (NIH/NIAID) [E] wrote:
> 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.
>

Hi,Barry. Thank you for your suggestion. Actually I am using the windows 
version of BLAST these days. The only inconvenience is that windows 
version of blast does not recognize the linux-like paths, as mentioned 
in my previous replies.

Now, it is solved after reading your reply. I was inspired by the notion 
of "convert cygwin's POSIX paths to Windows paths". I tried to convert 
the path into windows path using "cygpath -w" and it works smoothly. An 
example command line is as below:

blastall -p blastn -i nt.fas -d $(cygpath -w genome.db) -o test.out -m 8

I have modified the PATH variable so as to the blast programs could be 
automatically identified. genome.db is a soft link to the target 
database under the working directory. blastall can not interpret the 
soft link; but after translating the path using $(cygpath -w genome.db), 
it works perfectly.

Furthermore, there is in fact no need to create the linux-style soft 
link. I added a variable DB to store the windows-style path of the 
database and this makes a more simple solution.

DB="D:\Blast\blast-2.2.13\db\genome\genome.db"
blastall -p blastn -i nt.fas -d $DB -o test.out -m 8

Up to now, the problem is solved. Thanks to all that participated in the 
discussion. I should have make it clear that I just want to use the 
blast program under Cygwin. The efforts were diverted into two 
directions. One was to compile the program from source code. Many people 
contributed their ideas and the discussion deepened my understanding of 
Cygwin. The other was to use the windows version. The problem of 
different styles of paths was settled today. Thanks to all for your help.

Best regards,
DJ


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