[ensembl-dev] Problem in Running Ensembl Core API

[Urjaswita Yadav]

Hello Michael,

Thanks for your reply.

I have MySql client installed. I checked and MySql connection also works
properly. Unfortunately I still could not get the API working. I will give
virtual machine a try. Please let me know if you have any other suggestions.

Best Regards,
Urjaswita


On Mon, Nov 15, 2010 at 10:59 AM, Michael Schuster <michaels at ebi.ac.uk>wrote:

> 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/ <http://www.ebi.ac.uk/%7Emichaels/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/
>
>
>
>
>
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