[Bioperl-l] Question about HOWTO:StandAloneBlast

[Torsten Seemann]

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.

>  PATH=$PATH;C:\BLAST\BIN
>  BLASTDIR=C:\BLAST
>
> 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