[ensembl-dev] Problem in Running Ensembl Core API

Andreas Kahari ak at ebi.ac.uk
Mon Nov 15 09:43:19 GMT 2010


Hi Urjaswita,

How did you run the program?

The ID mapper code needs to be run with --species=human (for human, for
example), and with the input file either piped into standard input:

  IDmapper.pl --species=human < ./inputfile

or

  cat inputfile | IDmapper.pl --species=human

or by specifying with --file=inputfile what file to read:

  IDmapper.pl --species=human --file=inputfile

If only the species is specified, the program will not print anything
and will wait for input on standard input.

Note that I'm utterly unfamiliar with Windows, so I can not give any
Windows-specific help.


Andreas

On Sat, Nov 13, 2010 at 04:51:41PM +0100, 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




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-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom




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