[Bioperl-l] Question about HOWTO:StandAloneBlast

Mark A. Jensen maj at fortinbras.us
Thu Feb 19 22:06:43 EST 2009

----- Original Message ----- 
From: "Torsten Seemann" <torsten.seemann at gmail.com>
To: "bioperl-l" <Bioperl-l at lists.open-bio.org>
Cc: "Dongliang Wu" <donwu at med.umich.edu>
Sent: Thursday, February 19, 2009 8:41 PM
Subject: Re: [Bioperl-l] Question about HOWTO:StandAloneBlast

> Dongliang,
> Please submit questions to the bioperl-l at lists.open-bio.org mailing list.
>> I am writing to ask about a question regarding to locating the blastall.exe 
>> in windows.
>> Does following mean creating an autoexec.bat file containing the path? What 
>> does [fixme] mean? I am a neophyte of bioperl.
>> Windows: C:\AUTOEXEC.BAT [FIXME?]
> "FIXME" means that the author of the web page (myself) has left a
> message to himself that this web page is incomplete and needs fixing.
> As I don't use Windows, I wasn't 100% sure if those instructions were
> correct.
>> After running the autoexe.bat, I can execute the blastall.exe, but windows 
>> doesn't recognize perl as a command any more. How can I fix this path related 
>> problem?
> It seems doing the above has removed the Perl directory from your
> $PATH. To be honest, I do not know how to solve this Windows problem.
> Hopefully someone on this mailing list can enlighten me, and possibly
> update this page:
> http://www.bioperl.org/wiki/HOWTO:StandAloneBlast
> Thank you
> -- 
> --Torsten Seemann
> --Victorian Bioinformatics Consortium, Dept. Microbiology, Monash
> University, AUSTRALIA
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> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

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