Modifying the detail select menu in GBrowse2

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Modifying the detail select menu in GBrowse2

Scott Cain
Hi All,

Has anybody tried (and succeeded) at modifying the popup select menu
when a region is rubberband selected in the details panel?  In
GBrowse1, putting this in the conf file worked:

[DETAIL SELECT MENU]
width = 250
html  = <table style="width:100%">
         <tr>
           <th style="background:lightgrey;cell-padding:5">
             SELECTION
             <span style="right:0px;position:absolute;color:blue;cursor:pointer"
                   onclick="SelectArea.prototype.cancelRubber()">
               [X]
             </span>
           </th>
         </tr>
         <tr>
           <td>
             <span style="color:blue;cursor:pointer"
onclick="SelectArea.prototype.clearAndSubmit()">
              Zoom in
             </span>
           </td>
         </tr>
         <tr>
           <td>
             <span style="color:blue;cursor:pointer"
onclick="SelectArea.prototype.clearAndRecenter()">
               Recenter on this region
             </span>
           </td>
         </tr>
         <tr>
           <td onmouseup="SelectArea.prototype.cancelRubber()">
             <a href="/cgi-bin/apollo_request_region.pl?selection=SELECTION">
              Open this section in Apollo
             </a>
           </td>
         </tr>
       </table>

but it doesn't appear to work when put in either GBrowse.conf or the
database specific conf file for GBrowse2.

Thanks,
Scott



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: Modifying the detail select menu in GBrowse2

Jayaraman, Pushkala
Didn't Joao m. P. Alves do this for his Gbrowse so that he could dump data into Apollo?
Was that Gbrowse2?

Pushkala Jayaraman
Programmer/Analyst
Rat Genome Database
Human and Molecular Genetics Center
Medical College of Wisconsin
Email: [hidden email]
Work: 414-955-2229
www.rgd.mcw.edu


-----Original Message-----
From: Scott Cain [mailto:[hidden email]]
Sent: Thursday, September 09, 2010 10:20 PM
To: Gbrowse (E-mail)
Subject: [Gmod-gbrowse] Modifying the detail select menu in GBrowse2

Hi All,

Has anybody tried (and succeeded) at modifying the popup select menu
when a region is rubberband selected in the details panel?  In
GBrowse1, putting this in the conf file worked:

[DETAIL SELECT MENU]
width = 250
html  = <table style="width:100%">
         <tr>
           <th style="background:lightgrey;cell-padding:5">
             SELECTION
             <span style="right:0px;position:absolute;color:blue;cursor:pointer"
                   onclick="SelectArea.prototype.cancelRubber()">
               [X]
             </span>
           </th>
         </tr>
         <tr>
           <td>
             <span style="color:blue;cursor:pointer"
onclick="SelectArea.prototype.clearAndSubmit()">
              Zoom in
             </span>
           </td>
         </tr>
         <tr>
           <td>
             <span style="color:blue;cursor:pointer"
onclick="SelectArea.prototype.clearAndRecenter()">
               Recenter on this region
             </span>
           </td>
         </tr>
         <tr>
           <td onmouseup="SelectArea.prototype.cancelRubber()">
             <a href="/cgi-bin/apollo_request_region.pl?selection=SELECTION">
              Open this section in Apollo
             </a>
           </td>
         </tr>
       </table>

but it doesn't appear to work when put in either GBrowse.conf or the
database specific conf file for GBrowse2.

Thanks,
Scott



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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search string dependent configuration

DDI (FH) Andreas Redl
Hi all,

I was wondering if - when searching for a certain feature or landmark -  the
search string is available globally and can be used in the configuration. I
would like to colorize features that contain a specific search motif.
Thanks!

Best,

Andreas Redl


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Re: Modifying the detail select menu in GBrowse2

J.M.P. Alves
In reply to this post by Jayaraman, Pushkala
Hi,

Yes, I did that. I first did it in GBrowse 1.7, which is the one I
showed at the course. Now I have it, slightly different (no option for
opening Apollo, although that should work too), in GBrowse 2, for example:

http://www.gardnerella.mic.vcu.edu/
(click either of the Browsers links on the bottom left)

Is that what you were thinking of, Scott?

I added the [DETAIL SELECT MENU] stanza to the database specific conf
files. It did NOT work when I added it to the general GBrowse.conf. I
wish it had worked (with the possibility of overriding or adding to it
in the DB specific files), since I have that stanza in all my conf files.

By the way, mine looks like this:

[DETAIL SELECT MENU]
width = 300
html  = <table style="width:100%">
          <tr>
            <th style="background:lightgrey;cell-padding:5">
              SELECTION
              <span
style="right:0px;position:absolute;color:blue;cursor:pointer"
onclick="SelectArea.prototype.cancelRubber()"> [X] </span>
            </th>
          </tr>
          <tr>
            <td onmouseup="SelectArea.prototype.cancelRubber()">
              <a
href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION"
target="_BLANK"> Dump selection as FASTA </a>
            </td>
          </tr>
          <tr>
            <td onmouseup="SelectArea.prototype.cancelRubber()">
              <a
href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST"
target="_BLANK"> Submit selection to NCBI BLAST </a>
            </td>
          </tr>
          <tr>
            <td>
              <span style="color:blue;cursor:pointer"
onclick="SelectArea.prototype.clearAndSubmit()"> Zoom in </span>
            </td>
          </tr>
          <tr>
            <td>
              <span style="color:blue;cursor:pointer"
onclick="SelectArea.prototype.clearAndRecenter()"> Recenter on this
region </span>
            </td>
          </tr>
        </table>


Cheers
J

Jayaraman, Pushkala wrote:

> Didn't Joao m. P. Alves do this for his Gbrowse so that he could dump data into Apollo?
> Was that Gbrowse2?
>
> Pushkala Jayaraman
> Programmer/Analyst
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> Email: [hidden email]
> Work: 414-955-2229
> www.rgd.mcw.edu
>
>
> -----Original Message-----
> From: Scott Cain [mailto:[hidden email]]
> Sent: Thursday, September 09, 2010 10:20 PM
> To: Gbrowse (E-mail)
> Subject: [Gmod-gbrowse] Modifying the detail select menu in GBrowse2
>
> Hi All,
>
> Has anybody tried (and succeeded) at modifying the popup select menu
> when a region is rubberband selected in the details panel?  In
> GBrowse1, putting this in the conf file worked:
>
> [DETAIL SELECT MENU]
> width = 250
> html  = <table style="width:100%">
>          <tr>
>            <th style="background:lightgrey;cell-padding:5">
>              SELECTION
>              <span style="right:0px;position:absolute;color:blue;cursor:pointer"
>                    onclick="SelectArea.prototype.cancelRubber()">
>                [X]
>              </span>
>            </th>
>          </tr>
>          <tr>
>            <td>
>              <span style="color:blue;cursor:pointer"
> onclick="SelectArea.prototype.clearAndSubmit()">
>               Zoom in
>              </span>
>            </td>
>          </tr>
>          <tr>
>            <td>
>              <span style="color:blue;cursor:pointer"
> onclick="SelectArea.prototype.clearAndRecenter()">
>                Recenter on this region
>              </span>
>            </td>
>          </tr>
>          <tr>
>            <td onmouseup="SelectArea.prototype.cancelRubber()">
>              <a href="/cgi-bin/apollo_request_region.pl?selection=SELECTION">
>               Open this section in Apollo
>              </a>
>            </td>
>          </tr>
>        </table>
>
> but it doesn't appear to work when put in either GBrowse.conf or the
> database specific conf file for GBrowse2.
>
> Thanks,
> Scott
>
>
>

--
-------------------------------
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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automated storage tiering capabilities. View this brief to learn how
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Re: Modifying the detail select menu in GBrowse2

Scott Cain
Hi J,

Where did you put that stanza in the file?  I've tried a few things
and it doesn't seem to be working.

Scott


On Fri, Sep 10, 2010 at 11:43 AM, J.M.P. Alves <[hidden email]> wrote:

> Hi,
>
> Yes, I did that. I first did it in GBrowse 1.7, which is the one I showed at
> the course. Now I have it, slightly different (no option for opening Apollo,
> although that should work too), in GBrowse 2, for example:
>
> http://www.gardnerella.mic.vcu.edu/
> (click either of the Browsers links on the bottom left)
>
> Is that what you were thinking of, Scott?
>
> I added the [DETAIL SELECT MENU] stanza to the database specific conf files.
> It did NOT work when I added it to the general GBrowse.conf. I wish it had
> worked (with the possibility of overriding or adding to it in the DB
> specific files), since I have that stanza in all my conf files.
>
> By the way, mine looks like this:
>
> [DETAIL SELECT MENU]
> width = 300
> html  = <table style="width:100%">
>         <tr>
>           <th style="background:lightgrey;cell-padding:5">
>             SELECTION
>             <span
> style="right:0px;position:absolute;color:blue;cursor:pointer"
> onclick="SelectArea.prototype.cancelRubber()"> [X] </span>
>           </th>
>         </tr>
>         <tr>
>           <td onmouseup="SelectArea.prototype.cancelRubber()">
>             <a href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION"
> target="_BLANK"> Dump selection as FASTA </a>
>           </td>
>         </tr>
>         <tr>
>           <td onmouseup="SelectArea.prototype.cancelRubber()">
>             <a
> href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST"
> target="_BLANK"> Submit selection to NCBI BLAST </a>
>           </td>
>         </tr>
>         <tr>
>           <td>
>             <span style="color:blue;cursor:pointer"
> onclick="SelectArea.prototype.clearAndSubmit()"> Zoom in </span>
>           </td>
>         </tr>
>         <tr>
>           <td>
>             <span style="color:blue;cursor:pointer"
> onclick="SelectArea.prototype.clearAndRecenter()"> Recenter on this region
> </span>
>           </td>
>         </tr>
>       </table>
>
>
> Cheers
> J
>
> Jayaraman, Pushkala wrote:
>>
>> Didn't Joao m. P. Alves do this for his Gbrowse so that he could dump data
>> into Apollo?
>> Was that Gbrowse2?
>>
>> Pushkala Jayaraman
>> Programmer/Analyst
>> Rat Genome Database
>> Human and Molecular Genetics Center
>> Medical College of Wisconsin
>> Email: [hidden email]
>> Work: 414-955-2229
>> www.rgd.mcw.edu
>>
>>
>> -----Original Message-----
>> From: Scott Cain [mailto:[hidden email]] Sent: Thursday, September
>> 09, 2010 10:20 PM
>> To: Gbrowse (E-mail)
>> Subject: [Gmod-gbrowse] Modifying the detail select menu in GBrowse2
>>
>> Hi All,
>>
>> Has anybody tried (and succeeded) at modifying the popup select menu
>> when a region is rubberband selected in the details panel?  In
>> GBrowse1, putting this in the conf file worked:
>>
>> [DETAIL SELECT MENU]
>> width = 250
>> html  = <table style="width:100%">
>>         <tr>
>>           <th style="background:lightgrey;cell-padding:5">
>>             SELECTION
>>             <span
>> style="right:0px;position:absolute;color:blue;cursor:pointer"
>>                   onclick="SelectArea.prototype.cancelRubber()">
>>               [X]
>>             </span>
>>           </th>
>>         </tr>
>>         <tr>
>>           <td>
>>             <span style="color:blue;cursor:pointer"
>> onclick="SelectArea.prototype.clearAndSubmit()">
>>              Zoom in
>>             </span>
>>           </td>
>>         </tr>
>>         <tr>
>>           <td>
>>             <span style="color:blue;cursor:pointer"
>> onclick="SelectArea.prototype.clearAndRecenter()">
>>               Recenter on this region
>>             </span>
>>           </td>
>>         </tr>
>>         <tr>
>>           <td onmouseup="SelectArea.prototype.cancelRubber()">
>>             <a
>> href="/cgi-bin/apollo_request_region.pl?selection=SELECTION">
>>              Open this section in Apollo
>>             </a>
>>           </td>
>>         </tr>
>>       </table>
>>
>> but it doesn't appear to work when put in either GBrowse.conf or the
>> database specific conf file for GBrowse2.
>>
>> Thanks,
>> Scott
>>
>>
>>
>
> --
> -------------------------------
> João Marcelo Pereira Alves (J)
> Post-doctoral fellow
> MCV / VCU - Richmond, VA
> http://bioinfo.lpb.mic.vcu.edu
> f. 1-804-828-3897
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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automated storage tiering capabilities. View this brief to learn how
you can reduce costs and improve performance.
http://p.sf.net/sfu/dell-sfdev2dev
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Re: Modifying the detail select menu in GBrowse2

J.M.P. Alves
Hi, Scott

Yeah, I think I remember location mattering here... I put it just after
the [GENERAL], for example (partial file):

[GENERAL]
description   = Gardnerella vaginalis strain 5-1
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor DBI::mysql
                 -dsn   dbi:mysql:database=GVAMD
                 -user www-data

initial landmark = ADAM01000002:230000..260000

default tracks =   Genes
                   tRNAs
                   CDS

# examples to show in the introduction
examples = ADAM01000003
           ADAM01000008:80,000..90,000
           "carboxylate reductase"
           GVAMD_0010
           EFH28150

# "automatic" classes to try when an unqualified identifier is given
automatic classes = gene contig

[OVERVIEW SELECT MENU]
width = 300
html  = <table style="width:100%">
          <tr>
            <th style="background:lightgrey;cell-padding:5">
              SELECTION
              <span
style="right:0px;position:absolute;color:blue;cursor:pointer"
onclick="SelectArea.prototype.canc
elRubber()"> [X] </span>
            </th>
          </tr>
          <tr>
            <td>
              <span style="color:blue;cursor:pointer"
onclick="SelectArea.prototype.clearAndSubmit()"> Zoom </span>
            </td>
          </tr>
          <tr>
            <td onmouseup="SelectArea.prototype.cancelRubber()">
              <a
href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION"
target="_BLANK"> Dump selection as FASTA
  </a>
            </td>
          </tr>
        </table>

[DETAIL SELECT MENU]
width = 300
html  = <table style="width:100%">
          <tr>
            <th style="background:lightgrey;cell-padding:5">
              SELECTION
              <span
style="right:0px;position:absolute;color:blue;cursor:pointer"
onclick="SelectArea.prototype.cancelRubber()"> [X] </span>
            </th>
          </tr>
          <tr>
            <td onmouseup="SelectArea.prototype.cancelRubber()">
              <a
href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION"
target="_BLANK"> Dump selection as FASTA </a>
            </td>
          </tr>
          <tr>
            <td onmouseup="SelectArea.prototype.cancelRubber()">
              <a
href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST"
target="_BLANK"> Submit selection to NCBI BLAST </a>
            </td>
          </tr>
          <tr>
            <td>
              <span style="color:blue;cursor:pointer"
onclick="SelectArea.prototype.clearAndSubmit()"> Zoom in </span>
            </td>
          </tr>
          <tr>
            <td>
              <span style="color:blue;cursor:pointer"
onclick="SelectArea.prototype.clearAndRecenter()"> Recenter on this
region </span>
            </td>
          </tr>
        </table>

[Submitter:plugin]
submitter = [NCBI_BLAST]
             confirm   = 1
             url       = http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
             seq_label = QUERY
             PAGE      = Nucleotides
             extra_html = BLAST type:
                          <SELECT name="PROGRAM">
                            <OPTION VALUE="blastn">blastn</OPTION>
                            <OPTION VALUE="blastx">blastx</OPTION>
                            <OPTION VALUE="tblastx">tblastx</OPTION>
                          </SELECT><BR>
                          Database:
                          <SELECT name="DATABASE">
                            <OPTION VALUE="nr">nr/nt</OPTION>
                            <OPTION VALUE="est">est</OPTION>
                            <OPTION VALUE="refseq_rna">refseq_rna</OPTION>
                            <OPTION
VALUE="refseq_genomic">refseq_genomic</OPTION>
                            <OPTION VALUE="env_nt">env_nt</OPTION>
                            <OPTION VALUE="chromosome">chromosome</OPTION>
                          </SELECT><br>
                          E-value threshold: <input name="EXPECT"
size="10" type="text" value="1e-6"><br>
                          Filter low complexity regions <input
type="checkbox" name="FILTER" value="L" checked><br>
                          Mask for lookup table only <input
type="checkbox" name="FILTER" value="m" checked><br>
                          Mask lower case letters <input type="checkbox"
name="LCASE_MASK"><br>
             CLIENT    = web
             CMD       = put


[TOOLTIPS]
full_sequence = sub {
                   my $args = shift;
                   my $feat = $args->{feature};
                   my $name  = $feat->display_name;
                   my $seq = $feat->seq->seq;
                   $seq =~ s/(\S{75})/$1\n/g;
                   return "<pre>>$name\n$seq</pre>";
                }



# Default glyph settings

etc. etc.

If I remember correctly, the [TOOLTIPS] stanza was needed for the "get
FASTA" and "BLAST this" functionality to work, but I can't remember if
its absence precluded the menu from appearing. You might want to try
adding that if you haven't already.

Take care
J


Scott Cain wrote:

> Hi J,
>
> Where did you put that stanza in the file?  I've tried a few things
> and it doesn't seem to be working.
>
> Scott
>
>
> On Fri, Sep 10, 2010 at 11:43 AM, J.M.P. Alves <[hidden email]> wrote:
>> Hi,
>>
>> Yes, I did that. I first did it in GBrowse 1.7, which is the one I showed at
>> the course. Now I have it, slightly different (no option for opening Apollo,
>> although that should work too), in GBrowse 2, for example:
>>
>> http://www.gardnerella.mic.vcu.edu/
>> (click either of the Browsers links on the bottom left)
>>
>> Is that what you were thinking of, Scott?
>>
>> I added the [DETAIL SELECT MENU] stanza to the database specific conf files.
>> It did NOT work when I added it to the general GBrowse.conf. I wish it had
>> worked (with the possibility of overriding or adding to it in the DB
>> specific files), since I have that stanza in all my conf files.
>>
>> By the way, mine looks like this:
>>
>> [DETAIL SELECT MENU]
>> width = 300
>> html  = <table style="width:100%">
>>         <tr>
>>           <th style="background:lightgrey;cell-padding:5">
>>             SELECTION
>>             <span
>> style="right:0px;position:absolute;color:blue;cursor:pointer"
>> onclick="SelectArea.prototype.cancelRubber()"> [X] </span>
>>           </th>
>>         </tr>
>>         <tr>
>>           <td onmouseup="SelectArea.prototype.cancelRubber()">
>>             <a href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION"
>> target="_BLANK"> Dump selection as FASTA </a>
>>           </td>
>>         </tr>
>>         <tr>
>>           <td onmouseup="SelectArea.prototype.cancelRubber()">
>>             <a
>> href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST"
>> target="_BLANK"> Submit selection to NCBI BLAST </a>
>>           </td>
>>         </tr>
>>         <tr>
>>           <td>
>>             <span style="color:blue;cursor:pointer"
>> onclick="SelectArea.prototype.clearAndSubmit()"> Zoom in </span>
>>           </td>
>>         </tr>
>>         <tr>
>>           <td>
>>             <span style="color:blue;cursor:pointer"
>> onclick="SelectArea.prototype.clearAndRecenter()"> Recenter on this region
>> </span>
>>           </td>
>>         </tr>
>>       </table>
>>
>>
>> Cheers
>> J
>>
>> Jayaraman, Pushkala wrote:
>>> Didn't Joao m. P. Alves do this for his Gbrowse so that he could dump data
>>> into Apollo?
>>> Was that Gbrowse2?
>>>
>>> Pushkala Jayaraman
>>> Programmer/Analyst
>>> Rat Genome Database
>>> Human and Molecular Genetics Center
>>> Medical College of Wisconsin
>>> Email: [hidden email]
>>> Work: 414-955-2229
>>> www.rgd.mcw.edu
>>>
>>>
>>> -----Original Message-----
>>> From: Scott Cain [mailto:[hidden email]] Sent: Thursday, September
>>> 09, 2010 10:20 PM
>>> To: Gbrowse (E-mail)
>>> Subject: [Gmod-gbrowse] Modifying the detail select menu in GBrowse2
>>>
>>> Hi All,
>>>
>>> Has anybody tried (and succeeded) at modifying the popup select menu
>>> when a region is rubberband selected in the details panel?  In
>>> GBrowse1, putting this in the conf file worked:
>>>
>>> [DETAIL SELECT MENU]
>>> width = 250
>>> html  = <table style="width:100%">
>>>         <tr>
>>>           <th style="background:lightgrey;cell-padding:5">
>>>             SELECTION
>>>             <span
>>> style="right:0px;position:absolute;color:blue;cursor:pointer"
>>>                   onclick="SelectArea.prototype.cancelRubber()">
>>>               [X]
>>>             </span>
>>>           </th>
>>>         </tr>
>>>         <tr>
>>>           <td>
>>>             <span style="color:blue;cursor:pointer"
>>> onclick="SelectArea.prototype.clearAndSubmit()">
>>>              Zoom in
>>>             </span>
>>>           </td>
>>>         </tr>
>>>         <tr>
>>>           <td>
>>>             <span style="color:blue;cursor:pointer"
>>> onclick="SelectArea.prototype.clearAndRecenter()">
>>>               Recenter on this region
>>>             </span>
>>>           </td>
>>>         </tr>
>>>         <tr>
>>>           <td onmouseup="SelectArea.prototype.cancelRubber()">
>>>             <a
>>> href="/cgi-bin/apollo_request_region.pl?selection=SELECTION">
>>>              Open this section in Apollo
>>>             </a>
>>>           </td>
>>>         </tr>
>>>       </table>
>>>
>>> but it doesn't appear to work when put in either GBrowse.conf or the
>>> database specific conf file for GBrowse2.
>>>
>>> Thanks,
>>> Scott
>>>
>>>
>>>
>> --
>> -------------------------------
>> João Marcelo Pereira Alves (J)
>> Post-doctoral fellow
>> MCV / VCU - Richmond, VA
>> http://bioinfo.lpb.mic.vcu.edu
>> f. 1-804-828-3897
>>
>>
>
>
>

--
-------------------------------
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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Re: Modifying the detail select menu in GBrowse2

Scott Cain
Hi J,

Thanks, actually, I think the problem was Firefox aggressively caching
(something--javascript probably).  When I opened GBrowse in Safari
(which I hadn't used for GBrowse), I got the correct popup.

Thanks,
Scott


On Fri, Sep 10, 2010 at 12:20 PM, J.M.P. Alves <[hidden email]> wrote:

> Hi, Scott
>
> Yeah, I think I remember location mattering here... I put it just after the
> [GENERAL], for example (partial file):
>
> [GENERAL]
> description   = Gardnerella vaginalis strain 5-1
> db_adaptor    = Bio::DB::SeqFeature::Store
> db_args       = -adaptor DBI::mysql
>                -dsn   dbi:mysql:database=GVAMD
>                -user www-data
>
> initial landmark = ADAM01000002:230000..260000
>
> default tracks =   Genes
>                   tRNAs
>                   CDS
>
> # examples to show in the introduction
> examples = ADAM01000003
>           ADAM01000008:80,000..90,000
>           "carboxylate reductase"
>           GVAMD_0010
>           EFH28150
>
> # "automatic" classes to try when an unqualified identifier is given
> automatic classes = gene contig
>
> [OVERVIEW SELECT MENU]
> width = 300
> html  = <table style="width:100%">
>         <tr>
>           <th style="background:lightgrey;cell-padding:5">
>             SELECTION
>             <span
> style="right:0px;position:absolute;color:blue;cursor:pointer"
> onclick="SelectArea.prototype.canc
> elRubber()"> [X] </span>
>           </th>
>         </tr>
>         <tr>
>           <td>
>             <span style="color:blue;cursor:pointer"
> onclick="SelectArea.prototype.clearAndSubmit()"> Zoom </span>
>           </td>
>         </tr>
>         <tr>
>           <td onmouseup="SelectArea.prototype.cancelRubber()">
>             <a href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION"
> target="_BLANK"> Dump selection as FASTA
>  </a>
>           </td>
>         </tr>
>       </table>
>
> [DETAIL SELECT MENU]
> width = 300
> html  = <table style="width:100%">
>         <tr>
>           <th style="background:lightgrey;cell-padding:5">
>             SELECTION
>             <span
> style="right:0px;position:absolute;color:blue;cursor:pointer"
> onclick="SelectArea.prototype.cancelRubber()"> [X] </span>
>           </th>
>         </tr>
>         <tr>
>           <td onmouseup="SelectArea.prototype.cancelRubber()">
>             <a href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION"
> target="_BLANK"> Dump selection as FASTA </a>
>           </td>
>         </tr>
>         <tr>
>           <td onmouseup="SelectArea.prototype.cancelRubber()">
>             <a
> href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST"
> target="_BLANK"> Submit selection to NCBI BLAST </a>
>           </td>
>         </tr>
>         <tr>
>           <td>
>             <span style="color:blue;cursor:pointer"
> onclick="SelectArea.prototype.clearAndSubmit()"> Zoom in </span>
>           </td>
>         </tr>
>         <tr>
>           <td>
>             <span style="color:blue;cursor:pointer"
> onclick="SelectArea.prototype.clearAndRecenter()"> Recenter on this region
> </span>
>           </td>
>         </tr>
>       </table>
>
> [Submitter:plugin]
> submitter = [NCBI_BLAST]
>            confirm   = 1
>            url       = http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
>            seq_label = QUERY
>            PAGE      = Nucleotides
>            extra_html = BLAST type:
>                         <SELECT name="PROGRAM">
>                           <OPTION VALUE="blastn">blastn</OPTION>
>                           <OPTION VALUE="blastx">blastx</OPTION>
>                           <OPTION VALUE="tblastx">tblastx</OPTION>
>                         </SELECT><BR>
>                         Database:
>                         <SELECT name="DATABASE">
>                           <OPTION VALUE="nr">nr/nt</OPTION>
>                           <OPTION VALUE="est">est</OPTION>
>                           <OPTION VALUE="refseq_rna">refseq_rna</OPTION>
>                           <OPTION
> VALUE="refseq_genomic">refseq_genomic</OPTION>
>                           <OPTION VALUE="env_nt">env_nt</OPTION>
>                           <OPTION VALUE="chromosome">chromosome</OPTION>
>                         </SELECT><br>
>                         E-value threshold: <input name="EXPECT" size="10"
> type="text" value="1e-6"><br>
>                         Filter low complexity regions <input type="checkbox"
> name="FILTER" value="L" checked><br>
>                         Mask for lookup table only <input type="checkbox"
> name="FILTER" value="m" checked><br>
>                         Mask lower case letters <input type="checkbox"
> name="LCASE_MASK"><br>
>            CLIENT    = web
>            CMD       = put
>
>
> [TOOLTIPS]
> full_sequence = sub {
>                  my $args = shift;
>                  my $feat = $args->{feature};
>                  my $name  = $feat->display_name;
>                  my $seq = $feat->seq->seq;
>                  $seq =~ s/(\S{75})/$1\n/g;
>                  return "<pre>>$name\n$seq</pre>";
>               }
>
>
>
> # Default glyph settings
>
> etc. etc.
>
> If I remember correctly, the [TOOLTIPS] stanza was needed for the "get
> FASTA" and "BLAST this" functionality to work, but I can't remember if its
> absence precluded the menu from appearing. You might want to try adding that
> if you haven't already.
>
> Take care
> J
>
>
> Scott Cain wrote:
>>
>> Hi J,
>>
>> Where did you put that stanza in the file?  I've tried a few things
>> and it doesn't seem to be working.
>>
>> Scott
>>
>>
>> On Fri, Sep 10, 2010 at 11:43 AM, J.M.P. Alves <[hidden email]> wrote:
>>>
>>> Hi,
>>>
>>> Yes, I did that. I first did it in GBrowse 1.7, which is the one I showed
>>> at
>>> the course. Now I have it, slightly different (no option for opening
>>> Apollo,
>>> although that should work too), in GBrowse 2, for example:
>>>
>>> http://www.gardnerella.mic.vcu.edu/
>>> (click either of the Browsers links on the bottom left)
>>>
>>> Is that what you were thinking of, Scott?
>>>
>>> I added the [DETAIL SELECT MENU] stanza to the database specific conf
>>> files.
>>> It did NOT work when I added it to the general GBrowse.conf. I wish it
>>> had
>>> worked (with the possibility of overriding or adding to it in the DB
>>> specific files), since I have that stanza in all my conf files.
>>>
>>> By the way, mine looks like this:
>>>
>>> [DETAIL SELECT MENU]
>>> width = 300
>>> html  = <table style="width:100%">
>>>        <tr>
>>>          <th style="background:lightgrey;cell-padding:5">
>>>            SELECTION
>>>            <span
>>> style="right:0px;position:absolute;color:blue;cursor:pointer"
>>> onclick="SelectArea.prototype.cancelRubber()"> [X] </span>
>>>          </th>
>>>        </tr>
>>>        <tr>
>>>          <td onmouseup="SelectArea.prototype.cancelRubber()">
>>>            <a href="?plugin=FastaDumper;plugin_action=Go;name=SELECTION"
>>> target="_BLANK"> Dump selection as FASTA </a>
>>>          </td>
>>>        </tr>
>>>        <tr>
>>>          <td onmouseup="SelectArea.prototype.cancelRubber()">
>>>            <a
>>>
>>> href="?name=SELECTION;plugin=Submitter;plugin_do=Go;Submitter.target=NCBI_BLAST"
>>> target="_BLANK"> Submit selection to NCBI BLAST </a>
>>>          </td>
>>>        </tr>
>>>        <tr>
>>>          <td>
>>>            <span style="color:blue;cursor:pointer"
>>> onclick="SelectArea.prototype.clearAndSubmit()"> Zoom in </span>
>>>          </td>
>>>        </tr>
>>>        <tr>
>>>          <td>
>>>            <span style="color:blue;cursor:pointer"
>>> onclick="SelectArea.prototype.clearAndRecenter()"> Recenter on this
>>> region
>>> </span>
>>>          </td>
>>>        </tr>
>>>      </table>
>>>
>>>
>>> Cheers
>>> J
>>>
>>> Jayaraman, Pushkala wrote:
>>>>
>>>> Didn't Joao m. P. Alves do this for his Gbrowse so that he could dump
>>>> data
>>>> into Apollo?
>>>> Was that Gbrowse2?
>>>>
>>>> Pushkala Jayaraman
>>>> Programmer/Analyst
>>>> Rat Genome Database
>>>> Human and Molecular Genetics Center
>>>> Medical College of Wisconsin
>>>> Email: [hidden email]
>>>> Work: 414-955-2229
>>>> www.rgd.mcw.edu
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: Scott Cain [mailto:[hidden email]] Sent: Thursday, September
>>>> 09, 2010 10:20 PM
>>>> To: Gbrowse (E-mail)
>>>> Subject: [Gmod-gbrowse] Modifying the detail select menu in GBrowse2
>>>>
>>>> Hi All,
>>>>
>>>> Has anybody tried (and succeeded) at modifying the popup select menu
>>>> when a region is rubberband selected in the details panel?  In
>>>> GBrowse1, putting this in the conf file worked:
>>>>
>>>> [DETAIL SELECT MENU]
>>>> width = 250
>>>> html  = <table style="width:100%">
>>>>        <tr>
>>>>          <th style="background:lightgrey;cell-padding:5">
>>>>            SELECTION
>>>>            <span
>>>> style="right:0px;position:absolute;color:blue;cursor:pointer"
>>>>                  onclick="SelectArea.prototype.cancelRubber()">
>>>>              [X]
>>>>            </span>
>>>>          </th>
>>>>        </tr>
>>>>        <tr>
>>>>          <td>
>>>>            <span style="color:blue;cursor:pointer"
>>>> onclick="SelectArea.prototype.clearAndSubmit()">
>>>>             Zoom in
>>>>            </span>
>>>>          </td>
>>>>        </tr>
>>>>        <tr>
>>>>          <td>
>>>>            <span style="color:blue;cursor:pointer"
>>>> onclick="SelectArea.prototype.clearAndRecenter()">
>>>>              Recenter on this region
>>>>            </span>
>>>>          </td>
>>>>        </tr>
>>>>        <tr>
>>>>          <td onmouseup="SelectArea.prototype.cancelRubber()">
>>>>            <a
>>>> href="/cgi-bin/apollo_request_region.pl?selection=SELECTION">
>>>>             Open this section in Apollo
>>>>            </a>
>>>>          </td>
>>>>        </tr>
>>>>      </table>
>>>>
>>>> but it doesn't appear to work when put in either GBrowse.conf or the
>>>> database specific conf file for GBrowse2.
>>>>
>>>> Thanks,
>>>> Scott
>>>>
>>>>
>>>>
>>> --
>>> -------------------------------
>>> João Marcelo Pereira Alves (J)
>>> Post-doctoral fellow
>>> MCV / VCU - Richmond, VA
>>> http://bioinfo.lpb.mic.vcu.edu
>>> f. 1-804-828-3897
>>>
>>>
>>
>>
>>
>
> --
> -------------------------------
> João Marcelo Pereira Alves (J)
> Post-doctoral fellow
> MCV / VCU - Richmond, VA
> http://bioinfo.lpb.mic.vcu.edu
> f. 1-804-828-3897
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Optimize IT performance and efficiency through flexible, powerful,
automated storage tiering capabilities. View this brief to learn how
you can reduce costs and improve performance.
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_______________________________________________
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