execute blastall from cgi-bin

Olga Belenkiy olga.belenkiy at weizmann.ac.il
Fri Aug 16 03:28:53 EST 2002


What happened is that you got confused. Take another look at 
$ENV{'BLASTDB'}. It is defined as "/home/amir/Blast/data", however, in 
the error_log file the path is "/home/amir/Blast/Db/". The last 
directory in the error file is "Db" and not "data".

Olga.

amir orlev wrote:

>I've been trying to run blastall from a CGI script on a Linux (RH 7.2)
>machine.  The blastall program and Apache web server are on the same
>machine.
>I can run the program via perl scripts or from the command line
>without problem.  But when I create the cgi script and execute it from
>the web page I get the  error message in my httpd error_log file :
>
>[blastall] WARNING: eyal: Could not find index files for database
>/home/amir/Blast/Db/gbhuman.fa
>
>I've already used formatdb to create these index files.  The correct
>path is given in the CGI script:
>       system "/usr/local/bin/blastall  -p blastp....."
>
>The .ncbirc file has been created with appropriate paths for Data.
>     .
>     .
>    [NCBI]
>     Data=/home/amir/Blast/data
>
>To make sure that the paths are correct, I defined the 2 environment
>variables as follows:
>
>$ENV{'BLASTDB'} = "/home/amir/Blast/data";
>$ENV{'NCBI'} = "/home/amir";
>
>How can I fix the problem ??? can someone help me ?
>I will appreciate your help ...
>
>Thank, Amir.
>  
>

-- 

Olga Belenkiy

Molecular Genetics dept.         | olga.belenkiy at weizmann.ac.il
Weizmann Institute of Science,   | fax: ##972 (8) 934 4108
POBox 26, Rehovot 76100, Israel. | tel: ##972 (8) 934 4911
        http://bioinformatics.weizmann.ac.il/~olgab





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