[ensembl-dev] Problem in Running Ensembl Core API

[Will Spooner]

On 15 Nov 2010, at 22:16, Urjaswita Yadav wrote:

> 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.

There are also Ensembl VMWare VMs available here;

http://www.eaglegenomics.com/download/

Will


> 
> 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/
> 
> 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>_______________________________________________
> 
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> 
> --
> 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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--
William Spooner
whs at eaglegenomics.com
http://www.eaglegenomics.com