[Gmod-ajax] Upgrading to current jbrowse with jbrowse.conf issues

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[Gmod-ajax] Upgrading to current jbrowse with jbrowse.conf issues

Hans Vasquez-Gross
Hi All,

   I just upgraded my jbrowse instance to 1.11.2 from a previous version that didn't have the new jbrowse.conf and only had jbrowse_conf.json. I followed the normal update procedure by migrating my data directory to the new jbrowse folder.  After editing the configurations, I am still getting the following error:

SyntaxError: Unexpected token - when parsing jbrowse_conf.json.

However, in the distribution, the jbrowse_conf.json file is blank by default.


##My Configurations
[jbrowse.conf]
[GENERAL]

## edit this include statement to load and merge in more configuration files
include  = {dataRoot}/json/tilling/trackList.json

 [datasets.tilling]
 url  = ?data=data/json/tilling
 name = Wheat TILLING



##OLD jbrowse_conf.json configuration
[old jbrowse_conf.json]  (I left the default blank jbrowse_conf.json and, just edited the new jbrowse.conf file)
// JBrowse JSON-format configuration file
{

    datasets: {
        tilling:    { url: '?data=data/json/tilling', name: 'Wheat TILLING' },
    }
}

 I tried turning on the JS console, but couldn't dig any deeper into the "Unexpected token  error".  An example URL that used to work is http://169.237.215.34/jbrowse/?data=data%2Fjson%2Ftilling&loc=UCW_012911.1%3A1..229&tracks=DNA%2Cmysnps&highlight=

Any advice would be appreciated. 

Cheers,
-Hans

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Re: Upgrading to current jbrowse with jbrowse.conf issues

Richard Hayes
Is that blank line above the "datasets" section of your old jbrowse_conf.json in the file, too?

I find I get error messages like "unexpected token" when there is unintended whitespace in the configuration. That definitely can be a problem with the jbrowse.conf (and tracks.conf) config style, but I'm not certain that this will effect the JSON files in the same way.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Wed, Feb 19, 2014 at 12:45 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi All,

   I just upgraded my jbrowse instance to 1.11.2 from a previous version that didn't have the new jbrowse.conf and only had jbrowse_conf.json. I followed the normal update procedure by migrating my data directory to the new jbrowse folder.  After editing the configurations, I am still getting the following error:

SyntaxError: Unexpected token - when parsing jbrowse_conf.json.

However, in the distribution, the jbrowse_conf.json file is blank by default.


##My Configurations
[jbrowse.conf]
[GENERAL]

## edit this include statement to load and merge in more configuration files
include  = {dataRoot}/json/tilling/trackList.json

 [datasets.tilling]
 url  = ?data=data/json/tilling
 name = Wheat TILLING



##OLD jbrowse_conf.json configuration
[old jbrowse_conf.json]  (I left the default blank jbrowse_conf.json and, just edited the new jbrowse.conf file)
// JBrowse JSON-format configuration file
{

    datasets: {
        tilling:    { url: '?data=data/json/tilling', name: 'Wheat TILLING' },
    }
}

 I tried turning on the JS console, but couldn't dig any deeper into the "Unexpected token  error".  An example URL that used to work is http://169.237.215.34/jbrowse/?data=data%2Fjson%2Ftilling&loc=UCW_012911.1%3A1..229&tracks=DNA%2Cmysnps&highlight=

Any advice would be appreciated. 

Cheers,
-Hans

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Re: Upgrading to current jbrowse with jbrowse.conf issues

Richard Hayes
Hi,

No, to answer my own question, the JSON format is more forgiving about whitespace. So, there is something else going on.

When I tried to view your example URL, I got a genome region with no tracks configured. If you are up for sharing the full config files in question as email attachments, I can take another look.


Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Wed, Feb 19, 2014 at 2:04 PM, Richard Hayes <[hidden email]> wrote:
Is that blank line above the "datasets" section of your old jbrowse_conf.json in the file, too?

I find I get error messages like "unexpected token" when there is unintended whitespace in the configuration. That definitely can be a problem with the jbrowse.conf (and tracks.conf) config style, but I'm not certain that this will effect the JSON files in the same way.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Wed, Feb 19, 2014 at 12:45 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi All,

   I just upgraded my jbrowse instance to 1.11.2 from a previous version that didn't have the new jbrowse.conf and only had jbrowse_conf.json. I followed the normal update procedure by migrating my data directory to the new jbrowse folder.  After editing the configurations, I am still getting the following error:

SyntaxError: Unexpected token - when parsing jbrowse_conf.json.

However, in the distribution, the jbrowse_conf.json file is blank by default.


##My Configurations
[jbrowse.conf]
[GENERAL]

## edit this include statement to load and merge in more configuration files
include  = {dataRoot}/json/tilling/trackList.json

 [datasets.tilling]
 url  = ?data=data/json/tilling
 name = Wheat TILLING



##OLD jbrowse_conf.json configuration
[old jbrowse_conf.json]  (I left the default blank jbrowse_conf.json and, just edited the new jbrowse.conf file)
// JBrowse JSON-format configuration file
{

    datasets: {
        tilling:    { url: '?data=data/json/tilling', name: 'Wheat TILLING' },
    }
}

 I tried turning on the JS console, but couldn't dig any deeper into the "Unexpected token  error".  An example URL that used to work is http://169.237.215.34/jbrowse/?data=data%2Fjson%2Ftilling&loc=UCW_012911.1%3A1..229&tracks=DNA%2Cmysnps&highlight=

Any advice would be appreciated. 

Cheers,
-Hans

------------------------------------------------------------------------------
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Re: Upgrading to current jbrowse with jbrowse.conf issues

Hans Vasquez-Gross
Hi Richard,

  Thank you for the offer.  I've attached the configuration files.   I'll explain how my current directory layout is structured (which worked for the previous version).

In the main jbrowse/ directory on the webserver:
  • the blank jbrowse_conf.json(attached) that ships with jbrowse
  • jbrowse.conf (attached)
In jbrowse/data/ directory on the webserver:
  • json/tilling/ and vcf_files/tilling/ directory
  • vcf_files directory has the vcf and tbi file
  • json/tilling directory has trackList.json(attached), tracks.conf (attached)
  • json/tilling directory has a seq directory with the refSeqs.json and sequence sub-directories
I organized the data in this manner, so I can easily add another project.  I realized that my old trackList.json may be creating some collision with the new tracks.conf and jbrowse.conf configuration method.  Thank you again for giving some input.

Cheers,
-Hans


On Wed, Feb 19, 2014 at 2:09 PM, Richard Hayes <[hidden email]> wrote:
Hi,

No, to answer my own question, the JSON format is more forgiving about whitespace. So, there is something else going on.

When I tried to view your example URL, I got a genome region with no tracks configured. If you are up for sharing the full config files in question as email attachments, I can take another look.


Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Wed, Feb 19, 2014 at 2:04 PM, Richard Hayes <[hidden email]> wrote:
Is that blank line above the "datasets" section of your old jbrowse_conf.json in the file, too?

I find I get error messages like "unexpected token" when there is unintended whitespace in the configuration. That definitely can be a problem with the jbrowse.conf (and tracks.conf) config style, but I'm not certain that this will effect the JSON files in the same way.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Wed, Feb 19, 2014 at 12:45 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi All,

   I just upgraded my jbrowse instance to 1.11.2 from a previous version that didn't have the new jbrowse.conf and only had jbrowse_conf.json. I followed the normal update procedure by migrating my data directory to the new jbrowse folder.  After editing the configurations, I am still getting the following error:

SyntaxError: Unexpected token - when parsing jbrowse_conf.json.

However, in the distribution, the jbrowse_conf.json file is blank by default.


##My Configurations
[jbrowse.conf]
[GENERAL]

## edit this include statement to load and merge in more configuration files
include  = {dataRoot}/json/tilling/trackList.json

 [datasets.tilling]
 url  = ?data=data/json/tilling
 name = Wheat TILLING



##OLD jbrowse_conf.json configuration
[old jbrowse_conf.json]  (I left the default blank jbrowse_conf.json and, just edited the new jbrowse.conf file)
// JBrowse JSON-format configuration file
{

    datasets: {
        tilling:    { url: '?data=data/json/tilling', name: 'Wheat TILLING' },
    }
}

 I tried turning on the JS console, but couldn't dig any deeper into the "Unexpected token  error".  An example URL that used to work is http://169.237.215.34/jbrowse/?data=data%2Fjson%2Ftilling&loc=UCW_012911.1%3A1..229&tracks=DNA%2Cmysnps&highlight=

Any advice would be appreciated. 

Cheers,
-Hans

------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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--
Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Phone: (530) 752-0609
Skype: hansvg.ucd

------------------------------------------------------------------------------
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jbrowse_conf.json (410 bytes) Download Attachment
jbrowse.conf (2K) Download Attachment
trackList.json (824 bytes) Download Attachment
tracks.conf (652 bytes) Download Attachment
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Re: Upgrading to current jbrowse with jbrowse.conf issues

Hans Vasquez-Gross
After looking at the link I provided you after clearing the cache, I was able to get the genome region interface as well.  However, no data loads.  Looking at the console, it seems to be configured to look in the wrong directory. 

When it should be going to 



I tried trimming off '/json/tilling' in my jbrowse.conf for the datasets definition, but it didn't seem to fix the problem.

Cheers,
-Hans


On Wed, Feb 19, 2014 at 2:20 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi Richard,

  Thank you for the offer.  I've attached the configuration files.   I'll explain how my current directory layout is structured (which worked for the previous version).

In the main jbrowse/ directory on the webserver:
  • the blank jbrowse_conf.json(attached) that ships with jbrowse
  • jbrowse.conf (attached)
In jbrowse/data/ directory on the webserver:
  • json/tilling/ and vcf_files/tilling/ directory
  • vcf_files directory has the vcf and tbi file
  • json/tilling directory has trackList.json(attached), tracks.conf (attached)
  • json/tilling directory has a seq directory with the refSeqs.json and sequence sub-directories
I organized the data in this manner, so I can easily add another project.  I realized that my old trackList.json may be creating some collision with the new tracks.conf and jbrowse.conf configuration method.  Thank you again for giving some input.

Cheers,
-Hans


On Wed, Feb 19, 2014 at 2:09 PM, Richard Hayes <[hidden email]> wrote:
Hi,

No, to answer my own question, the JSON format is more forgiving about whitespace. So, there is something else going on.

When I tried to view your example URL, I got a genome region with no tracks configured. If you are up for sharing the full config files in question as email attachments, I can take another look.


Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Wed, Feb 19, 2014 at 2:04 PM, Richard Hayes <[hidden email]> wrote:
Is that blank line above the "datasets" section of your old jbrowse_conf.json in the file, too?

I find I get error messages like "unexpected token" when there is unintended whitespace in the configuration. That definitely can be a problem with the jbrowse.conf (and tracks.conf) config style, but I'm not certain that this will effect the JSON files in the same way.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Wed, Feb 19, 2014 at 12:45 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi All,

   I just upgraded my jbrowse instance to 1.11.2 from a previous version that didn't have the new jbrowse.conf and only had jbrowse_conf.json. I followed the normal update procedure by migrating my data directory to the new jbrowse folder.  After editing the configurations, I am still getting the following error:

SyntaxError: Unexpected token - when parsing jbrowse_conf.json.

However, in the distribution, the jbrowse_conf.json file is blank by default.


##My Configurations
[jbrowse.conf]
[GENERAL]

## edit this include statement to load and merge in more configuration files
include  = {dataRoot}/json/tilling/trackList.json

 [datasets.tilling]
 url  = ?data=data/json/tilling
 name = Wheat TILLING



##OLD jbrowse_conf.json configuration
[old jbrowse_conf.json]  (I left the default blank jbrowse_conf.json and, just edited the new jbrowse.conf file)
// JBrowse JSON-format configuration file
{

    datasets: {
        tilling:    { url: '?data=data/json/tilling', name: 'Wheat TILLING' },
    }
}

 I tried turning on the JS console, but couldn't dig any deeper into the "Unexpected token  error".  An example URL that used to work is http://169.237.215.34/jbrowse/?data=data%2Fjson%2Ftilling&loc=UCW_012911.1%3A1..229&tracks=DNA%2Cmysnps&highlight=

Any advice would be appreciated. 

Cheers,
-Hans

------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
_______________________________________________
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--
Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Phone: <a href="tel:%28530%29%20752-0609" value="+15307520609" target="_blank">(530) 752-0609
Skype: hansvg.ucd



--
Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Phone: (530) 752-0609
Skype: hansvg.ucd

------------------------------------------------------------------------------
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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
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Re: Upgrading to current jbrowse with jbrowse.conf issues

Hans Vasquez-Gross
I fixed it by messing with my configurations more.  Thank you for pointing me in the correct direction.

Cheers,
-Hans


On Wed, Feb 19, 2014 at 2:45 PM, Hans Vasquez-Gross <[hidden email]> wrote:
After looking at the link I provided you after clearing the cache, I was able to get the genome region interface as well.  However, no data loads.  Looking at the console, it seems to be configured to look in the wrong directory. 

When it should be going to 



I tried trimming off '/json/tilling' in my jbrowse.conf for the datasets definition, but it didn't seem to fix the problem.

Cheers,
-Hans


On Wed, Feb 19, 2014 at 2:20 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi Richard,

  Thank you for the offer.  I've attached the configuration files.   I'll explain how my current directory layout is structured (which worked for the previous version).

In the main jbrowse/ directory on the webserver:
  • the blank jbrowse_conf.json(attached) that ships with jbrowse
  • jbrowse.conf (attached)
In jbrowse/data/ directory on the webserver:
  • json/tilling/ and vcf_files/tilling/ directory
  • vcf_files directory has the vcf and tbi file
  • json/tilling directory has trackList.json(attached), tracks.conf (attached)
  • json/tilling directory has a seq directory with the refSeqs.json and sequence sub-directories
I organized the data in this manner, so I can easily add another project.  I realized that my old trackList.json may be creating some collision with the new tracks.conf and jbrowse.conf configuration method.  Thank you again for giving some input.

Cheers,
-Hans


On Wed, Feb 19, 2014 at 2:09 PM, Richard Hayes <[hidden email]> wrote:
Hi,

No, to answer my own question, the JSON format is more forgiving about whitespace. So, there is something else going on.

When I tried to view your example URL, I got a genome region with no tracks configured. If you are up for sharing the full config files in question as email attachments, I can take another look.


Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Wed, Feb 19, 2014 at 2:04 PM, Richard Hayes <[hidden email]> wrote:
Is that blank line above the "datasets" section of your old jbrowse_conf.json in the file, too?

I find I get error messages like "unexpected token" when there is unintended whitespace in the configuration. That definitely can be a problem with the jbrowse.conf (and tracks.conf) config style, but I'm not certain that this will effect the JSON files in the same way.

Richard D. Hayes, Ph.D.
Joint Genome Institute / Lawrence Berkeley National Lab
http://www.phytozome.net


On Wed, Feb 19, 2014 at 12:45 PM, Hans Vasquez-Gross <[hidden email]> wrote:
Hi All,

   I just upgraded my jbrowse instance to 1.11.2 from a previous version that didn't have the new jbrowse.conf and only had jbrowse_conf.json. I followed the normal update procedure by migrating my data directory to the new jbrowse folder.  After editing the configurations, I am still getting the following error:

SyntaxError: Unexpected token - when parsing jbrowse_conf.json.

However, in the distribution, the jbrowse_conf.json file is blank by default.


##My Configurations
[jbrowse.conf]
[GENERAL]

## edit this include statement to load and merge in more configuration files
include  = {dataRoot}/json/tilling/trackList.json

 [datasets.tilling]
 url  = ?data=data/json/tilling
 name = Wheat TILLING



##OLD jbrowse_conf.json configuration
[old jbrowse_conf.json]  (I left the default blank jbrowse_conf.json and, just edited the new jbrowse.conf file)
// JBrowse JSON-format configuration file
{

    datasets: {
        tilling:    { url: '?data=data/json/tilling', name: 'Wheat TILLING' },
    }
}

 I tried turning on the JS console, but couldn't dig any deeper into the "Unexpected token  error".  An example URL that used to work is http://169.237.215.34/jbrowse/?data=data%2Fjson%2Ftilling&loc=UCW_012911.1%3A1..229&tracks=DNA%2Cmysnps&highlight=

Any advice would be appreciated. 

Cheers,
-Hans

------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
http://pubads.g.doubleclick.net/gampad/clk?id=121054471&iu=/4140/ostg.clktrk
_______________________________________________
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--
Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Phone: <a href="tel:%28530%29%20752-0609" value="+15307520609" target="_blank">(530) 752-0609
Skype: hansvg.ucd



--
Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Phone: <a href="tel:%28530%29%20752-0609" value="+15307520609" target="_blank">(530) 752-0609
Skype: hansvg.ucd



--
Hans Vasquez-Gross
Programmer
Dubcovsky and Neale Lab
Department of Plant Science
University of California at Davis
Phone: (530) 752-0609
Skype: hansvg.ucd

------------------------------------------------------------------------------
Managing the Performance of Cloud-Based Applications
Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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Re: Upgrading to current jbrowse with jbrowse.conf issues

Hans Vasquez-Gross
Now that I've added a second dataset, I'm running into some more issues.  When loading my initial dataset which worked (http://169.237.215.34/jbrowse/?data=data%2Fjson%2Ftilling&loc=UCW_041346.1%3A1..3975&tracks=DNA%2Cmysnps&highlight=), the interface loads up with the correct tracks selected.   However, when zooming into the sequence track, the sequencing data isn't retrieved because it is trying to get the seq data from the other dataset.  When commenting out my configuration for the second dataset, it is able to load the sequencing data for the first dataset.

200 OK
7.34s
dojo.js (line 355)
RequestError: Unable to load data/json/tilling/names/root.json status: 404
dojo.js (line 141)


You can see on the last line from the log, it is searching in the wrong directory.  Is it because I essentially have the same DNA track defined in each dataset's trackList.json?  In my data/ directory, I have the json sub-directory.  In this subdirectory, I have two folders: tilling and iwgsc-tilling each with it's own seq reference.  
data/json/
     tilling/
          trackList.json
          seq/

    iwgsc-tilling/
         trackList.json
         seq/

I've attached my configuration files.  Thank you for any input.

Cheers,
-Hans



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jbrowse.conf (3K) Download Attachment
trackList.json (316 bytes) Download Attachment
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Re: Upgrading to current jbrowse with jbrowse.conf issues

Robert Buels-2
Did this issue get resolved OK?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 02/19/2014 07:35 PM, Hans Vasquez-Gross wrote:
> Now that I've added a second dataset, I'm running into some more issues.
>   When loading my initial dataset which worked
> (http://169.237.215.34/jbrowse/?data=data%2Fjson%2Ftilling&loc=UCW_041346.1%3A1..3975&tracks=DNA%2Cmysnps&highlight=),
> the interface loads up with the correct tracks selected.   However, when
> zooming into the sequence track, the sequencing data isn't retrieved
> because it is trying to get the seq data from the other dataset.  When
> commenting out my configuration for the second dataset, it is able to
> load the sequencing data for the first dataset.

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Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
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Re: Upgrading to current jbrowse with jbrowse.conf issues

Hans Vasquez-Gross
Yes, it's resolved.

Thank you,
-Hans


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Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
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