[Bioperl-l] Problem using Bio::Tools::Run::RemoteBlast

Carnë Draug carandraug+dev at gmail.com
Wed Sep 7 12:47:16 EDT 2011

2011/8/27 Lucky Singh <slucky at ibab.ac.in>:
> On Friday 26 August 2011 07:50 PM, Carnė Draug wrote:
>> On 22 August 2011 07:01, Lucky Singh<slucky at ibab.ac.in>  wrote:
>>> Now I
>>> wanted to host it from web server, but This program is not working from
>>> it
>>> may be it is not able to create or write on file from web server but in
>>> command line it is working fine. I don't know the possible reason, please
>>> help me to figure it out.
>> Have you looked in the apache logs (look in
>> /var/log/apache2/error.log) ? Can you pastebin your whole code and the
>> content of the error log after trying to run the script?
> Dear Carnė Draug,
> As per your suggestion, I am attaching blast code file currently it is not
> showing any error on error.log.
> Thanks a lot for your valuable reply and will be highly grateful if you can
> get me out of this problem :)


sorry for the late reply. Please try to always reply to the mailing
list, maybe someone else can help you too. I don't know about the
script as I never used RemoteBlast from bioperl. But given a quick
look at it, you're not loading the CGI module on the script (
http://perldoc.perl.org/CGI.html ). Here's a simple example using the
CGI module ( http://pastebin.com/miMd70wn ) and a HTML page that will
use it ( http://pastebin.com/kWwwMijd ).

If nothing shows up on error.log, take a look in access.log. Try some
simple CGI script first, such as "hello world!" to see if the problem
lies on your bioperl part of the script, or in the web server, or some
other part.


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