[Bioperl-l] newbie tries StandAloneBlast and receives "cant open BLOSUM62"

Harald haralds_listen at gmx.de
Thu Mar 2 15:48:12 EST 2006

Good idea!

By the way, the instructions are the same for Windows 2000 and the SET 
command is also present under NT4 and Windows 2000. And I would skip the 
sentences "Some versions of Windows may have problems differentiating 
forward and back slashes used for directories. In general, always use 
backslashes (\). If something isn't working properly try reversing the 
slashes to see if it helps.". This is not true. In Windows the '\' is 
the one and only directory separator known from the system. On 
Unix/Linux it is '/'

 I can not add it to the Wiki entry because, I have no account ( and 
doubt that a newbie like me could be of any further help :-/ ).

But this BLASTDIR variable confuses me. I have not set this variable, I 
have just set the bin-directory of my blast installation into the PATH 
environment variable. And my blastall and blastpgp seem to work probably 
with BioPerl.

Besides, the info given in 
http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows#BLAST differs 
from my experience. The only installing instructions I found reside in 
the doc-directory of my blast 2.2.13 install and there is no file called 
README.bls. And the problem with the docs is, that it is not mentioned 
(as far as I can see), that you have to put the bin-directory onto the 
PATH variable. This is bad, since copying e.g. blastall.exe into the 
current working directory (thus circumventing the need of the PATH 
variable to start blastall) leads to the problem I mentioned initially.

Is this BLASTDIR only relevant for BioPerl-1.5 ? (I am using 1.4)


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