BioMart / ProServer

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BioMart / ProServer

Charles Imbusch
Hi,

I'm locally running a BioMart (v 0.7) and I'm quite amazed by it's
functionality.

I loaded a set of genomic contigs into the database, which I can also
access by MartView.
Now I'm stuck at bringing ProServer and BioMart together with a minimal
working configuration. At the moment the only attributes I have for the
contig dataset, are the id's and it's sequence.

I set up an importable/exportable pair so that ProServer can access the
data. ProServer is then complaining with the following message:

Recieved filt contigID_key
Error building adaptor 'Bio::Das::ProServer::SourceAdaptor::biomart' for
'mymart1': BioMart DAS Compliant feature_keys list must contain at least
id,type,method
 at blib/lib/Bio/Das/ProServer.pm line 794

I read that "type" could be "Chromosome", "contig", ... Does that mean I
need to add a new field to my database where every entry is "contig"? Does
the same apply to the "method" field?

Does maybe an existing example configuration for BioMart/ProServer exist?

Any help would be appreciated,
  Charles

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Re: BioMart / ProServer

Joachim Baran
Hi!

On 4 November 2010 10:29, Charles Imbusch <[hidden email]> wrote:
> Does maybe an existing example configuration for BioMart/ProServer exist?
  Is the build-in DAS-server of BioMart not sufficient enough for you?
It actually works fairly well.

  If you want to plug-in a DAS-track into the Ensembl-browser, you
need to make some modifications though. You have to provide a SOURCES
command as well, which has been hacked into BioMart 0.7 by me:
https://github.com/joejimbo/biomart-plus-extras A lot is hardcoded,
but I am sure you could modify it to your needs.

Best Wishes,
Joachim

--
B.1079 Michael Smith Building
Faculty of Life Sciences
The University of Manchester
Oxford Road
Manchester
M13 9PT
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Re: BioMart / ProServer

Syed Haider
Hi Charles,

Yes, please state your use cases, generally DAS feature requested is
sufficient for most cases and you can use it out of the box from
BioMart, by just setting some attribtues and filters that you need to be
in the DAS response.

thanks,
Syed

On 04/11/2010 11:35, Joachim Baran wrote:

> Hi!
>
> On 4 November 2010 10:29, Charles Imbusch<[hidden email]>  wrote:
>> Does maybe an existing example configuration for BioMart/ProServer exist?
>    Is the build-in DAS-server of BioMart not sufficient enough for you?
> It actually works fairly well.
>
>    If you want to plug-in a DAS-track into the Ensembl-browser, you
> need to make some modifications though. You have to provide a SOURCES
> command as well, which has been hacked into BioMart 0.7 by me:
> https://github.com/joejimbo/biomart-plus-extras A lot is hardcoded,
> but I am sure you could modify it to your needs.
>
> Best Wishes,
> Joachim
>
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Re: BioMart / ProServer

Charles Imbusch
In reply to this post by Joachim Baran
Hello Joachim

>   Is the build-in DAS-server of BioMart not sufficient enough for you?
> It actually works fairly well.

Maybe I missed something, but I thought ProServer is the common DAS server to
work with BioMart.

>   If you want to plug-in a DAS-track into the Ensembl-browser, you
> need to make some modifications though. You have to provide a SOURCES
> command as well, which has been hacked into BioMart 0.7 by me:
> https://github.com/joejimbo/biomart-plus-extras A lot is hardcoded,
> but I am sure you could modify it to your needs.

That's actually not my intension, but I'll keep it in mind.

Cheers,
  Charles


suo
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install from remote

suo
Hello All,

Is there a way to install/set up mart from a remote machine other than on the server?
Thanks.


     
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Re: BioMart / ProServer

Joachim Baran
In reply to this post by Charles Imbusch
Hi!

On 5 November 2010 08:01, Charles Imbusch <[hidden email]> wrote:
> Maybe I missed something, but I thought ProServer is the common DAS server to
> work with BioMart.
  As far as I understand it, ProServer works with BioMart and there
are examples on how to customise it for a mart. However, in section
6.10 "DAS Server" of the BioMart 0.7 documentation
(http://www.biomart.org/user-docs.pdf) it gives examples that work
just out of the box. It might just be the case that a ProServer
installation allows you a more versatile approach towards solving your
problem.

Best Wishes,
Joachim


--
B.1079 Michael Smith Building
Faculty of Life Sciences
The University of Manchester
Oxford Road
Manchester
M13 9PT
United Kingdom
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Re: install from remote

Syed Haider
In reply to this post by suo
Hi Suo,

If i understand the problem correctly, its certainly possible to install
BioMart server on machine other than your local computer. All you need
to do is to 'ssh' into the server and do the installation as usual.

Let me know if there is any specific aspect of installation you need to
know.

Best,
Syed

On 05/11/2010 17:11, suo wrote:
> Hello All,
>
> Is there a way to install/set up mart from a remote machine other than on the server?
> Thanks.
>
>
>
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Re: BioMart / ProServer

Charles Imbusch
In reply to this post by Syed Haider
Hi Syed,

I would like to use the combination of BioMart / ProServer / GBrowse to
maintain and visualize
genomic assemblies and maybe more data later on.

To understand how to setup BioMart / ProServer I'm using the dataset
included in

http://gmod.org/wiki/BioMart_Tutorial

With MartEditor I created an importable/exportable pair with internalName,
displayName, linkName and name set to "mypair". I set the "type" field to
"dasGene" for both. For importable I set the filters field to
"stable_id_1023" and for exportable, I set the attributes to
"stable_id_1023,seq_region_start_1020,seq_region_end_1020,biotype_1020,source_1018".

For the ProServer configuration, I set:


feature_keys = id,start,end,type,method

Calling ProServer from a webbrowser causes an error:

Use of uninitialized value $call in string eq at
blib/lib/Bio/Das/ProServer.pm line 859.

Connection parameters of [My BioMart Database] [ OK ]

default ... My BioMart Database ...... 001/001 ... mydemo
.................................... (RDBMS) localhost:3306
................  OK
Setting possible links between datasets
....(scanning) 100%
....(linking) 100%
....(sorting) 100%
....(clustering) 1/1 - 0 remain
....(resolving) 100%
Error building adaptor 'Bio::Das::ProServer::SourceAdaptor::biomart' for
'mymart1': Can't call method "getImportables" on an undefined value at
/usr/local/share/perl/5.10.0/Bio/Das/ProServer/SourceAdaptor/biomart.pm
line 84.
 at blib/lib/Bio/Das/ProServer.pm line 794


Okay, this is not an BioMart specific, but maybe someone has a clue what's
going on.

Cheers,
  Charles


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Re: BioMart / ProServer

Syed Haider
Hi Charles,

Firstly, the Proserver component in the BioMart source code is
deprecated and not functional at all. Please do not use, i dont think
its document anywhere in project docs. BioMart DAS server is elsewhere
in the source and is documented in detail in project docs.

Could you please tell us which DAS features in particular are you
looking for ?

Thanks
Syed

On 08/11/2010 10:43, Charles Imbusch wrote:

> Hi Syed,
>
> I would like to use the combination of BioMart / ProServer / GBrowse to
> maintain and visualize
> genomic assemblies and maybe more data later on.
>
> To understand how to setup BioMart / ProServer I'm using the dataset
> included in
>
> http://gmod.org/wiki/BioMart_Tutorial
>
> With MartEditor I created an importable/exportable pair with internalName,
> displayName, linkName and name set to "mypair". I set the "type" field to
> "dasGene" for both. For importable I set the filters field to
> "stable_id_1023" and for exportable, I set the attributes to
> "stable_id_1023,seq_region_start_1020,seq_region_end_1020,biotype_1020,source_1018".
>
> For the ProServer configuration, I set:
>
>
> feature_keys = id,start,end,type,method
>
> Calling ProServer from a webbrowser causes an error:
>
> Use of uninitialized value $call in string eq at
> blib/lib/Bio/Das/ProServer.pm line 859.
>
> Connection parameters of [My BioMart Database] [ OK ]
>
> default ... My BioMart Database ...... 001/001 ... mydemo
> .................................... (RDBMS) localhost:3306
> ................  OK
> Setting possible links between datasets
> ....(scanning) 100%
> ....(linking) 100%
> ....(sorting) 100%
> ....(clustering) 1/1 - 0 remain
> ....(resolving) 100%
> Error building adaptor 'Bio::Das::ProServer::SourceAdaptor::biomart' for
> 'mymart1': Can't call method "getImportables" on an undefined value at
> /usr/local/share/perl/5.10.0/Bio/Das/ProServer/SourceAdaptor/biomart.pm
> line 84.
>   at blib/lib/Bio/Das/ProServer.pm line 794
>
>
> Okay, this is not an BioMart specific, but maybe someone has a clue what's
> going on.
>
> Cheers,
>    Charles
>
>
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Re: BioMart / ProServer

Charles Imbusch
Hi Syed and Joachim

> Firstly, the Proserver component in the BioMart source code is
> deprecated and not functional at all. Please do not use, i dont think
> its document anywhere in project docs. BioMart DAS server is elsewhere
> in the source and is documented in detail in project docs.

Ouch, not using Proserver at all is the solution ;-) Works fine now.
So actually there is no reason for keeping the "das" folder in the BioMart
distribution is there?

Cheers,
  Charles

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Re: BioMart / ProServer

Syed Haider
Hi Charles,


On 12/11/2010 07:46, Charles Imbusch wrote:

> Hi Syed and Joachim
>
>> Firstly, the Proserver component in the BioMart source code is
>> deprecated and not functional at all. Please do not use, i dont think
>> its document anywhere in project docs. BioMart DAS server is elsewhere
>> in the source and is documented in detail in project docs.
>
> Ouch, not using Proserver at all is the solution ;-) Works fine now.
> So actually there is no reason for keeping the "das" folder in the BioMart
> distribution is there?

Yes, ditto. Next release will have it removed.

Best,
Syed

>
> Cheers,
>    Charles
>