[ensembl-dev] Problem in Running Ensembl Core API

[Michael Schuster]

Hi Urjaswita,

I'm not using Windows myself so can't help you in detail, but you need  
to make sure you also have the MySQL client installed that the  
DBI::mysql module depends on. Further to that all firewalls on your  
computer and your institution need to allow outgoing TCP/IP  
connections to port 5306. The TCP/IP port 5306 is used for the public  
MySQL instance ensembldb.ensembl.org for databases since release 42,  
while 3306 is used for older data sets.

So the following has to work:

:~> mysql -u anonymous -h ensembldb.ensembl.org -P 5306
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 209764
Server version: 5.1.34-log Source distribution

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql>

Please note that MySQL communication is independent from proxies,  
which handle http, https and ftp requests.


This is about as far as we can support Windows users. However,  
recently we began experimenting with virtual machines. The idea is  
that you would have to install software allowing you to run virtual  
machines and then to import a machine image which runs GNU-Linux, the  
operating system we also use and has the Ensembl APIs pre-installed.

If you wanted to give this a try, a test image for Ensembl version 59  
would be here:

http://www.ebi.ac.uk/~michaels/vm/

You would have to install VirtualBox to run it. For a description what  
it does, how to install it on Windows and how to import a virtual  
appliance, please refer to the following pages:

http://www.virtualbox.org/

Hope that helps,
Michael



On 13 Nov 2010, at 15:51, Urjaswita Yadav wrote:

> Dear List Members,
>
> This maybe a bit naive question since i am using Ensembl API for the  
> first time. While trying to setup the Ensembl API, I followed the  
> instructions and I guess it installed correctly. I also have Bioperl  
> and DBI installed.
>
> But when I am trying to use any script e.g. Idmapper.pl (ftp://ftp.ensembl.org/pub/misc-scripts/ID_mapper_1.0/ 
> ) it does not do anything. It neither prints any output nor any  
> error message. I tried some other scripts too but the response is  
> same: no error and no output, it just remains executing. It even  
> does not prints a statement that I write at the top of program.
>
> This might be a problem with proxy but I am not sure as I am able to  
> ping Ensembl database but am not able to connect to it using a  
> database client like SQLyog. However I am able to download files  
> from internet using LWP::Simple. While browsing the internet using  
> mozilla I select "No proxy" or "autodetect proxy" for the network.
>
> I am using Windows XP. It would be a great help if anyone could  
> suggest anything. The programs I tried are attached.
>
> Thanks in anticipation.
>
> Best Regards,
> Urjaswita
> < 
> IDmapper 
> .pl 
> > 
> < 
> LWPtest 
> .pl><idmapper.in>_______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

--
Michael Schuster
Ensembl Genome Browser
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridgeshire CB10 1SD
United Kingdom

http://www.ensembl.org/