[Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

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[Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

anja
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Re: data are not displayed even though they were loaded (JBrowse)

Mitch Skinner
I'm not totally sure what's going on for you, but here's my best guess:

Usually, web servers are set up so that one particular path (e.g., /var/www) becomes the "root" of the space on the web server.  So, for example, if you put a file named "foo.html" into /var/www, so that the full path is /var/www/foo.html, then it'll show up in the web server as /foo.html.  So if you're accessing the web server on your laptop, you can see that HTML page by going to http://localhost/foo.html.

Different linux distributions put the "root" of the web server space in different places; in ubuntu (and distributions based on ubuntu, like Mint), it's /var/www.  In distributions derived from Red Hat, it's /var/www/html.

In your case, it looks like it's /var/www, so if you want to see what's in /var/www, you can visit http://localhost/ in your web browser.  If you look there, do you see your data?

Mitch

On 10/04/2010 11:52 AM, Anja Friedrich wrote:
Hi all,

I was using SeqFeature Store to load data and display them in JBrowse. But I an't see anything. They are not displayed at all like they don't exist... Do I activate it wrong? I was looking under http://localhost/jbrowse/
I used this commandos and it looks as if the data were loaded...

anou@anou-laptop:/var/www$ bp_seqfeature_load.pl --d "dbi:Pg:dbname=test" --a DBI::Pg --c taro.gff
loading taro.gff...
98 features loaded in  0.41s                                                    Building object tree... 0.02s
load time:  0.46s
anou@anou-laptop:/var/www$ bin/prepare-refseqs.pl --conf taro.json --refs NC_010109.1
anou@anou-laptop:/var/www$ bin/biodb-to-json.pl --conf taro.json

working on refseq NC_010109.1
working on track nested_tandem_repeat
got 1 features for nested_tandem_repeat
anou@anou-laptop:/var/www$ bin/generate-names.pl

Anja
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RE: data are not displayed even though they were loaded (JBrowse)

anja
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Re: data are not displayed even though they were loaded (JBrowse)

Mitch Skinner
  Do the motifs show up if you zoom in?

The motifs should show up, assuming that:

1. you have "subfeatures": true and "subfeature_classes" in your config
file, like this:

       "subfeatures": true,
       "subfeature_classes": {
         "motif1_small_a": "small_red",
         "motif1_small_b": "small_blue",
         "motif1_small_c": "small_purple",
         "motif1_tall_a": "tall_blue",
         "motif1_tall_b": "tall_purple"
       }

and 2. /var/www/genome.css has a listing for all of the values in the
"subfeature_classes" setting.

If have both of those things, then my best guess for what's going on is
this: by default, subfeatures like your motifs are only shown once you
zoom in beyond a certain level.

The threshold where they show up is controlled by the "subfeatureScale"
setting in the "clientConfig" part of the config file, so you can add
something like this:

       "clientConfig": {
           "subfeatureScale": 40
       },

The default is 80, and if you want the subfeatures to still show up when
you're more zoomed out, set it lower.

The actual units for the "subfeatureScale" setting are pixels/feature.  
That value is multiplied by the average feature density in features/base
units (i.e., the number of features in the track / the refseq length) to
get the scale threshold in pixels per base.  For example, if the
subfeatureScale is 2, and a track has 100 features, then subfeatures
will be shown if you're zoomed in far enough that the entire refseq
would be at least 200 pixels wide.

Hope this helps,
Mitch

On 10/05/2010 02:24 PM, anja wrote:
> Hi Mitch,
>
> when I visit http://localhost/ then I see the surface of JBrowse and
> the track as a grey line, so no motifs at all... more then before I guess


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RE: data are not displayed even though they were loaded (JBrowse)

anja
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Re: data are not displayed even though they were loaded (JBrowse)

Mitch Skinner
  Can you do this:

cd /var/www
tar czf taro-tracks.tar.gz data/tracks

That will create a file named taro-tracks.tar.gz, with your generated
data.  Then can you email the file to me?  That should help me figure
out what's going on.

Mitch


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Re: data are not displayed even though they were loaded (JBrowse)

Mitch Skinner
Okay, one of the GFF files that you sent earlier had strand information for the motifs.  I didn't notice that your later GFF files listed the motifs as being unstranded.

That's why, in the CSS example I sent earlier, the CSS classes were all listed with separate "plus-" and "minus-" versions.

If the motifs don't have strand information, then the CSS file should have CSS class names without those "plus-" and "minus-" prefixes.  For example, in the earlier example CSS file I sent, I had this:

=====
.plus-small_red,
.plus-small_blue,
.plus-small_purple,
.plus-tall_blue,
.plus-tall_purple,
.minus-small_red,
.minus-small_blue,
.minus-small_purple,
.minus-tall_blue,
.minus-tall_purple {
    position: absolute;
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

.plus-small_red, .minus-small_red {
    background-color: #EB2A2A; height: 6px; margin-top: -1px;
}
.plus-small_blue, .minus-small_blue {
    background-color: #46A1E0; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_purple {
    background-color: #7322BF; height: 6px; margin-top: -1px;
}
.plus-tall_blue, .minus-tall_blue {
    background-color: #46A1E0; height: 10px; margin-top: -3px;
}
.plus-tall_purple, .minus-tall_purple {
    background-color: #7322BF; height: 10px; margin-top: -3px;
}
=====


but if your motifs are unstranded, you could have this instead:


=====
.small_red,
.small_blue,
.small_purple,
.tall_blue,
.tall_purple {
    position: absolute;
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

.small_red {
    background-color: #EB2A2A; height: 6px; margin-top: -1px;
}
.small_blue {
    background-color: #46A1E0; height: 6px; margin-top: -1px;
}
.small_purple {
    background-color: #7322BF; height: 6px; margin-top: -1px;
}
.tall_blue {
    background-color: #46A1E0; height: 10px; margin-top: -3px;
}
.tall_purple {
    background-color: #7322BF; height: 10px; margin-top: -3px;
}
=====


Or, if your data has both stranded and unstranded features, you could include both stranded and unstranded versions of your CSS classes.

Mitch

On 10/05/2010 03:39 PM, Anja Friedrich wrote:
done

> Date: Tue, 5 Oct 2010 15:37:01 -0700
> From: [hidden email]
> To: [hidden email]; [hidden email]
> Subject: Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)
>
> Can you do this:
>
> cd /var/www
> tar czf taro-tracks.tar.gz data/tracks
>
> That will create a file named taro-tracks.tar.gz, with your generated
> data. Then can you email the file to me? That should help me figure
> out what's going on.
>
> Mitch
>


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Re: data are not displayed even though they were loaded (JBrowse)

anja
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Re: data are not displayed even though they were loaded (JBrowse)

Mitch Skinner
Hmmm, I know that we're very close, I tried out the data from your taro-tracks.tar.gz:

http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat

I noticed two things when I was setting that up; one was that the CSS file that you sent was named genome-2.css.  The index.html file has to refer to the correct CSS file.  In the index.html file, there's a line like this:

    <link rel="stylesheet" type="text/css" href="genome.css"></link>

I put your genome-2.css file in the same directory as the original genome.css, and changed that line in index.html to:

    <link rel="stylesheet" type="text/css" href="genome-2.css"></link>

Also, in the CSS file you sent, there was a line like this:

    .minus-tall_orange, {

which has an extra comma; it shouldn't have that comma at the end, like this:

    .minus-tall_orange {

or, if the data is unstranded, it should look like this:

    .tall_orange {


Also, some of the CSS classes were missing the "." at the beginning.

Mitch



On 10/06/2010 12:43 AM, Anja Friedrich wrote:
Thank you very much for your time and help.
I was afraid something like this will happen when I change it. But as I don't know whether they are stranded or not, I thought its better to mark it as unknown...
I changed all the classes but it still won't display the motifs. Do I have to change it somewhere in addition?

Anja

Date: Tue, 5 Oct 2010 18:31:31 -0700
From: [hidden email]
To: [hidden email]; [hidden email]
Subject: Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

Okay, one of the GFF files that you sent earlier had strand information for the motifs.  I didn't notice that your later GFF files listed the motifs as being unstranded.

That's why, in the CSS example I sent earlier, the CSS classes were all listed with separate "plus-" and "minus-" versions.

If the motifs don't have strand information, then the CSS file should have CSS class names without those "plus-" and "minus-" prefixes.  For example, in the earlier example CSS file I sent, I had this:

=====
.plus-small_red,
.plus-small_blue,
.plus-small_purple,
.plus-tall_blue,
.plus-tall_purple,
.minus-small_red,
.minus-small_blue,
.minus-small_purple,
.minus-tall_blue,
.minus-tall_purple {
    position: absolute;
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

.plus-small_red, .minus-small_red {
    background-color: #EB2A2A; height: 6px; margin-top: -1px;
}
.plus-small_blue, .minus-small_blue {
    background-color: #46A1E0; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_purple {
    background-color: #7322BF; height: 6px; margin-top: -1px;
}
.plus-tall_blue, .minus-tall_blue {
    background-color: #46A1E0; height: 10px; margin-top: -3px;
}
.plus-tall_purple, .minus-tall_purple {
    background-color: #7322BF; height: 10px; margin-top: -3px;
}
=====


but if your motifs are unstranded, you could have this instead:


=====
.small_red,
.small_blue,
.small_purple,
.tall_blue,
.tall_purple {
    position: absolute;
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

.small_red {
    background-color: #EB2A2A; height: 6px; margin-top: -1px;
}
.small_blue {
    background-color: #46A1E0; height: 6px; margin-top: -1px;
}
.small_purple {
    background-color: #7322BF; height: 6px; margin-top: -1px;
}
.tall_blue {
    background-color: #46A1E0; height: 10px; margin-top: -3px;
}
.tall_purple {
    background-color: #7322BF; height: 10px; margin-top: -3px;
}
=====


Or, if your data has both stranded and unstranded features, you could include both stranded and unstranded versions of your CSS classes.

Mitch

On 10/05/2010 03:39 PM, Anja Friedrich wrote:
done

> Date: Tue, 5 Oct 2010 15:37:01 -0700
> From: [hidden email]
> To: [hidden email]; [hidden email]
> Subject: Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)
>
> Can you do this:
>
> cd /var/www
> tar czf taro-tracks.tar.gz data/tracks
>
> That will create a file named taro-tracks.tar.gz, with your generated
> data. Then can you email the file to me? That should help me figure
> out what's going on.
>
> Mitch
>

------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb
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RE: data are not displayed even though they were loaded (JBrowse)

anja
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RE: data are not displayed even though they were loaded (JBrowse)

anja
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Re: data are not displayed even though they were loaded (JBrowse)

Mitch Skinner
The genome-2.css file is in /var/www?

On 10/06/2010 04:51 AM, anja wrote:
fixed everything but now I have a blank page...

Anja


Date: Wed, 6 Oct 2010 04:33:30 -0700
From: [hidden email]
To: [hidden email]
Subject: Re: data are not displayed even though they were loaded (JBrowse)

Hmmm, I know that we're very close, I tried out the data from your taro-tracks.tar.gz:

http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat

I noticed two things when I was setting that up; one was that the CSS file that you sent was named genome-2.css.  The index.html file has to refer to the correct CSS file.  In the index.html file, there's a line like this:

    <link rel="stylesheet" type="text/css" href="genome.css"></link>

I put your genome-2.css file in the same directory as the original genome.css, and changed that line in index.html to:

    <link rel="stylesheet" type="text/css" href="genome-2.css"></link>

Also, in the CSS file you sent, there was a line like this:

    .minus-tall_orange, {

which has an extra comma; it shouldn't have that comma at the end, like this:

    .minus-tall_orange {

or, if the data is unstranded, it should look like this:

    .tall_orange {


Also, some of the CSS classes were missing the "." at the beginning.

Mitch



On 10/06/2010 12:43 AM, Anja Friedrich wrote:
Thank you very much for your time and help.
I was afraid something like this will happen when I change it. But as I don't know whether they are stranded or not, I thought its better to mark it as unknown...
I changed all the classes but it still won't display the motifs. Do I have to change it somewhere in addition?

Anja

Date: Tue, 5 Oct 2010 18:31:31 -0700
From: [hidden email]
To: [hidden email]; [hidden email]
Subject: Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

Okay, one of the GFF files that you sent earlier had strand information for the motifs.  I didn't notice that your later GFF files listed the motifs as being unstranded.

That's why, in the CSS example I sent earlier, the CSS classes were all listed with separate "plus-" and "minus-" versions.

If the motifs don't have strand information, then the CSS file should have CSS class names without those "plus-" and "minus-" prefixes.  For example, in the earlier example CSS file I sent, I had this:

=====
.plus-small_red,
.plus-small_blue,
.plus-small_purple,
.plus-tall_blue,
.plus-tall_purple,
.minus-small_red,
.minus-small_blue,
.minus-small_purple,
.minus-tall_blue,
.minus-tall_purple {
    position: absolute;
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

.plus-small_red, .minus-small_red {
    background-color: #EB2A2A; height: 6px; margin-top: -1px;
}
.plus-small_blue, .minus-small_blue {
    background-color: #46A1E0; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_purple {
    background-color: #7322BF; height: 6px; margin-top: -1px;
}
.plus-tall_blue, .minus-tall_blue {
    background-color: #46A1E0; height: 10px; margin-top: -3px;
}
.plus-tall_purple, .minus-tall_purple {
    background-color: #7322BF; height: 10px; margin-top: -3px;
}
=====


but if your motifs are unstranded, you could have this instead:


=====
.small_red,
.small_blue,
.small_purple,
.tall_blue,
.tall_purple {
    position: absolute;
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

.small_red {
    background-color: #EB2A2A; height: 6px; margin-top: -1px;
}
.small_blue {
    background-color: #46A1E0; height: 6px; margin-top: -1px;
}
.small_purple {
    background-color: #7322BF; height: 6px; margin-top: -1px;
}
.tall_blue {
    background-color: #46A1E0; height: 10px; margin-top: -3px;
}
.tall_purple {
    background-color: #7322BF; height: 10px; margin-top: -3px;
}
=====


Or, if your data has both stranded and unstranded features, you could include both stranded and unstranded versions of your CSS classes.

Mitch

On 10/05/2010 03:39 PM, Anja Friedrich wrote:
done

> Date: Tue, 5 Oct 2010 15:37:01 -0700
> From: [hidden email]
> To: [hidden email]; [hidden email]
> Subject: Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)
>
> Can you do this:
>
> cd /var/www
> tar czf taro-tracks.tar.gz data/tracks
>
> That will create a file named taro-tracks.tar.gz, with your generated
> data. Then can you email the file to me? That should help me figure
> out what's going on.
>
> Mitch
>

------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb
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Spend less time writing and  rewriting code and more time creating great
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View this message in context: RE: data are not displayed even though they were loaded (JBrowse)
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RE: data are not displayed even though they were loaded (JBrowse)

anja
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Re: data are not displayed even though they were loaded (JBrowse)

Mitch Skinner
It has to be close.  Do this:

cd /var/www
tar czf taro.tar.gz *

and send me the taro.tar.gz.

Mitch

On 10/06/2010 04:59 AM, anja wrote:
yes


Date: Wed, 6 Oct 2010 04:56:55 -0700
From: [hidden email]
To: [hidden email]
Subject: Re: data are not displayed even though they were loaded (JBrowse)

The genome-2.css file is in /var/www?

On 10/06/2010 04:51 AM, anja wrote:
fixed everything but now I have a blank page...

Anja


Date: Wed, 6 Oct 2010 04:33:30 -0700
From: [hidden email]
To: [hidden email]
Subject: Re: data are not displayed even though they were loaded (JBrowse)

Hmmm, I know that we're very close, I tried out the data from your taro-tracks.tar.gz:

http://jbrowse.org/test/anja/?loc=NC_010109.1:939..2254&tracks=DNA,nested_tandem_repeat

I noticed two things when I was setting that up; one was that the CSS file that you sent was named genome-2.css.  The index.html file has to refer to the correct CSS file.  In the index.html file, there's a line like this:

    <link rel="stylesheet" type="text/css" href="genome.css"></link>

I put your genome-2.css file in the same directory as the original genome.css, and changed that line in index.html to:

    <link rel="stylesheet" type="text/css" href="genome-2.css"></link>

Also, in the CSS file you sent, there was a line like this:

    .minus-tall_orange, {

which has an extra comma; it shouldn't have that comma at the end, like this:

    .minus-tall_orange {

or, if the data is unstranded, it should look like this:

    .tall_orange {


Also, some of the CSS classes were missing the "." at the beginning.

Mitch



On 10/06/2010 12:43 AM, Anja Friedrich wrote:
Thank you very much for your time and help.
I was afraid something like this will happen when I change it. But as I don't know whether they are stranded or not, I thought its better to mark it as unknown...
I changed all the classes but it still won't display the motifs. Do I have to change it somewhere in addition?

Anja

Date: Tue, 5 Oct 2010 18:31:31 -0700
From: [hidden email]
To: [hidden email]; [hidden email]
Subject: Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)

Okay, one of the GFF files that you sent earlier had strand information for the motifs.  I didn't notice that your later GFF files listed the motifs as being unstranded.

That's why, in the CSS example I sent earlier, the CSS classes were all listed with separate "plus-" and "minus-" versions.

If the motifs don't have strand information, then the CSS file should have CSS class names without those "plus-" and "minus-" prefixes.  For example, in the earlier example CSS file I sent, I had this:

=====
.plus-small_red,
.plus-small_blue,
.plus-small_purple,
.plus-tall_blue,
.plus-tall_purple,
.minus-small_red,
.minus-small_blue,
.minus-small_purple,
.minus-tall_blue,
.minus-tall_purple {
    position: absolute;
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

.plus-small_red, .minus-small_red {
    background-color: #EB2A2A; height: 6px; margin-top: -1px;
}
.plus-small_blue, .minus-small_blue {
    background-color: #46A1E0; height: 6px; margin-top: -1px;
}
.plus-small_purple, .minus-small_purple {
    background-color: #7322BF; height: 6px; margin-top: -1px;
}
.plus-tall_blue, .minus-tall_blue {
    background-color: #46A1E0; height: 10px; margin-top: -3px;
}
.plus-tall_purple, .minus-tall_purple {
    background-color: #7322BF; height: 10px; margin-top: -3px;
}
=====


but if your motifs are unstranded, you could have this instead:


=====
.small_red,
.small_blue,
.small_purple,
.tall_blue,
.tall_purple {
    position: absolute;
    cursor: pointer;
    z-index: 10;
    min-width: 1px;
}

.small_red {
    background-color: #EB2A2A; height: 6px; margin-top: -1px;
}
.small_blue {
    background-color: #46A1E0; height: 6px; margin-top: -1px;
}
.small_purple {
    background-color: #7322BF; height: 6px; margin-top: -1px;
}
.tall_blue {
    background-color: #46A1E0; height: 10px; margin-top: -3px;
}
.tall_purple {
    background-color: #7322BF; height: 10px; margin-top: -3px;
}
=====


Or, if your data has both stranded and unstranded features, you could include both stranded and unstranded versions of your CSS classes.

Mitch

On 10/05/2010 03:39 PM, Anja Friedrich wrote:
done

> Date: Tue, 5 Oct 2010 15:37:01 -0700
> From: [hidden email]
> To: [hidden email]; [hidden email]
> Subject: Re: [Gmod-ajax] data are not displayed even though they were loaded (JBrowse)
>
> Can you do this:
>
> cd /var/www
> tar czf taro-tracks.tar.gz data/tracks
>
> That will create a file named taro-tracks.tar.gz, with your generated
> data. Then can you email the file to me? That should help me figure
> out what's going on.
>
> Mitch
>

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RE: data are not displayed even though they were loaded (JBrowse)

anja
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Re: data are not displayed even though they were loaded (JBrowse)

Mitch Skinner-2
  On 10/06/2010 05:14 AM, anja wrote:
> sent

I haven't received it; it might be too large to email.  If you can put
it online (this is your eventual goal, right?) then I could look to see
what's going on.  Otherwise, you can compare your setup to mine and see
what the differences are.

> There is something else I noticed by looking at your visualisation.
> For example are the first 3 variants small, but have the same size as
> a tall motif. The second tall motif is not displayed, there is just
> the grey line... What can be the reason for this?

It's a typo in your CSS; the second tall motif is being displayed at the
beginning, making the first 3 variants look tall.  The second tall motif
is a "tall purple" one, and in the CSS there's this:

=====
.tall_blue,
.tall_purple
.tall_red,
=====

That missing comma for tall_purple is what's causing it.

Mitch


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[Gmod-ajax] FW: data are not displayed even though they were loaded (JBrowse)

anja
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