Re: Configuring GBrowse_syn Data Source display

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Re: Configuring GBrowse_syn Data Source display

Wes Barris
On 14/12/2010 8:35 AM, Khan, Anar wrote:
> Hi
> Is it possible to prevent the ‘Data Source’ drop down from being displayed? I’d like to restrict users to certain GBrowse_syn alignments and prevent them from being able to browse the full set of
> alignments set up to date, since some are commercially sensitive.

show sources    = 0

does this for GBrowse.  Have you tried this for GBrowse_syn?

> Cheers,
> Anar
> ____________________________
> Anar Khan
> Bioinformatician
> *T*+64 3 489 9154
> *E*[hidden email]
> *AgResearch Limited*
> Invermay Agricultural Centre
> Puddle Alley, Private Bag 50034, Mosgiel, New Zealand
> *T *+64 3 489 3809 *F*+64 3 489 3739 www.agresearch.co.nz <http://www.agresearch.co.nz>
> Farming Food and Health.*First*
> /Te Ahuwhenua Te Kai me te Whai Ora. //Tuatahi/
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> *Attention: *The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential
> and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended
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Re: Configuring GBrowse_syn Data Source display

Khan, Anar
Hi Wes

That works a treat! Thanks very much (:

Anar

>
> Message: 3
> Date: Tue, 14 Dec 2010 13:16:51 +1000
> From: Wes Barris <[hidden email]>
> Subject: Re: [Gmod-gbrowse] Configuring GBrowse_syn Data Source
> display
> To: [hidden email]
> Message-ID: <[hidden email]>
> Content-Type: text/plain; charset="windows-1252"; format=flowed
>
> On 14/12/2010 8:35 AM, Khan, Anar wrote:
> > Hi
> > Is it possible to prevent the ?Data Source? drop down from being
> displayed? I?d like to restrict users to certain GBrowse_syn alignments
> and prevent them from being able to browse the full set of
> > alignments set up to date, since some are commercially sensitive.
>
> show sources    = 0
>
> does this for GBrowse.  Have you tried this for GBrowse_syn?
>
> > Cheers,
> > Anar
> > ____________________________
> > Anar Khan
> > Bioinformatician
> > *T*+64 3 489 9154
> > *E*[hidden email]
> > *AgResearch Limited*
> > Invermay Agricultural Centre
> > Puddle Alley, Private Bag 50034, Mosgiel, New Zealand
> > *T *+64 3 489 3809 *F*+64 3 489 3739 www.agresearch.co.nz
> <http://www.agresearch.co.nz>
> > Farming Food and Health.*First*
> > /Te Ahuwhenua Te Kai me te Whai Ora. //Tuatahi/
> >
> > ---------------------------------------------------------------------
> -----------------------------------------------------------------------
> ------------------------------------------------------------
> >
> > *Attention: *The information contained in this message and/or
> attachments from AgResearch Limited is intended only for the persons or
> entities to which it is addressed and may contain confidential
> > and/or privileged material. Any review, retransmission, dissemination
> or other use of, or taking of any action in reliance upon, this
> information by persons or entities other than the intended
> > recipients is prohibited by AgResearch Limited. If you have received
> this message in error, please notify the sender immediately.
> >
> > ---------------------------------------------------------------------
> -----------------------------------------------------------------------
> ------------------------------------------------------------
> >
>
>
> --
> Wes Barris
>

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Re: Configuring GBrowse_syn Data Source display

J.M.P. Alves
Hi,

That's how I have done it in the past too. But I would like to see more
granularity there, instead of the all or nothing it is now with "show
sources". Maybe someone has already suggested this in the past, and if
that's the case here  goes my little push to bring it back up to the
surface. ;-)

It would be nice to be able to define "groups" in GBrowse.conf, and then
  have a "group" attribute in the data source's stanza -- or whatever
the names of them things. Like:

[GVAMD]
description = Gardnerella vaginalis strain AMD
path = GVAMD.conf
group = gard

So, whenever someone visited GVAMD, they would see only other data
sources belonging to the same group (gard). Omitting the group in the
stanza could mean that that data source is to be always shown regardless
of which group is being accessed, for example. Or that it would show no
other data sources, making the "show sources" redundant -- but that
might not be as good from a backwards compatibility point of view.

Anyway, these are the quick thoughts for the morning, I hope they make
some sense...

Cheers
J


Khan, Anar wrote:

> Hi Wes
>
> That works a treat! Thanks very much (:
>
> Anar
>
>> Message: 3
>> Date: Tue, 14 Dec 2010 13:16:51 +1000
>> From: Wes Barris <[hidden email]>
>> Subject: Re: [Gmod-gbrowse] Configuring GBrowse_syn Data Source
>> display
>> To: [hidden email]
>> Message-ID: <[hidden email]>
>> Content-Type: text/plain; charset="windows-1252"; format=flowed
>>
>> On 14/12/2010 8:35 AM, Khan, Anar wrote:
>>> Hi
>>> Is it possible to prevent the ?Data Source? drop down from being
>> displayed? I?d like to restrict users to certain GBrowse_syn alignments
>> and prevent them from being able to browse the full set of
>>> alignments set up to date, since some are commercially sensitive.
>> show sources    = 0
>>
>> does this for GBrowse.  Have you tried this for GBrowse_syn?
>>
>>> Cheers,
>>> Anar
>>> ____________________________
>>> Anar Khan
>>> Bioinformatician
>>> *T*+64 3 489 9154
>>> *E*[hidden email]
>>> *AgResearch Limited*
>>> Invermay Agricultural Centre
>>> Puddle Alley, Private Bag 50034, Mosgiel, New Zealand
>>> *T *+64 3 489 3809 *F*+64 3 489 3739 www.agresearch.co.nz
>> <http://www.agresearch.co.nz>
>>> Farming Food and Health.*First*
>>> /Te Ahuwhenua Te Kai me te Whai Ora. //Tuatahi/
>>>
>>> ---------------------------------------------------------------------
>> -----------------------------------------------------------------------
>> ------------------------------------------------------------
>>> *Attention: *The information contained in this message and/or
>> attachments from AgResearch Limited is intended only for the persons or
>> entities to which it is addressed and may contain confidential
>>> and/or privileged material. Any review, retransmission, dissemination
>> or other use of, or taking of any action in reliance upon, this
>> information by persons or entities other than the intended
>>> recipients is prohibited by AgResearch Limited. If you have received
>> this message in error, please notify the sender immediately.
>>> ---------------------------------------------------------------------
>> -----------------------------------------------------------------------
>> ------------------------------------------------------------
>>
>> --
>> Wes Barris
>>
>
> ------------------------------------------------------------------------------
> Lotusphere 2011
> Register now for Lotusphere 2011 and learn how
> to connect the dots, take your collaborative environment
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--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897


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