[Gmod-ajax] JBrowse 1.12.1 installed correctly not loading data

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[Gmod-ajax] JBrowse 1.12.1 installed correctly not loading data

Matt Simenc-2
Hi, I installed JBrowse 1.12.1 as follows:

1. copied to my iMac at /Library/WebServer/Documents/jbrowse
2. ran setup.sh with the following output

Joshuas-iMac-2:jbrowse derstudent$ sudo ./setup.sh 

Installing Perl prerequisites ... done.


Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.


Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.


Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.


Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.


3. from the directory with index.html I ran prepare-refseq.pl --fasta mygenome.fa. a new directory "data" was created with a tracksList.json file and tracks.conf file

4. I pointed Safari at http://localhost/jbrowse/index.html and saw the following screen:

Inline image 1

5. I clicked the "Volvox test data here" link and JBrowse seems to be working fine with the Volvox data.


Can anyone help me get my data loaded? I have done everything indicated on the Quick-start Tutorial to get a refseq in a browser and can't find any information on the wikis about this SyntaxError. The file in /Library/WebServer/Documents/jbrowse/data/tracksList.json looks ok to me but I am new to json format.


Thank you!
Matt Simenc

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Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
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Re: JBrowse 1.12.1 installed correctly not loading data

grahammb

Dear Matt,

 

Do you mind sharing your trackList.json file with us? It should not be too large.

 

Thanks,

Mitchell

 

From: Matt Simenc [mailto:[hidden email]]
Sent: Monday, May 09, 2016 6:09 PM
To: [hidden email]
Subject: [Gmod-ajax] JBrowse 1.12.1 installed correctly not loading data

 

Hi, I installed JBrowse 1.12.1 as follows:

 

1. copied to my iMac at /Library/WebServer/Documents/jbrowse

2. ran setup.sh with the following output

 

Joshuas-iMac-2:jbrowse derstudent$ sudo ./setup.sh 

Installing Perl prerequisites ... done.

 

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

 

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

 

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

 

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

 

3. from the directory with index.html I ran prepare-refseq.pl --fasta mygenome.fa. a new directory "data" was created with a tracksList.json file and tracks.conf file

 

4. I pointed Safari at http://localhost/jbrowse/index.html and saw the following screen:

 

Inline image 1

 

5. I clicked the "Volvox test data here" link and JBrowse seems to be working fine with the Volvox data.

 

 

Can anyone help me get my data loaded? I have done everything indicated on the Quick-start Tutorial to get a refseq in a browser and can't find any information on the wikis about this SyntaxError. The file in /Library/WebServer/Documents/jbrowse/data/tracksList.json looks ok to me but I am new to json format.

 

 

Thank you!

Matt Simenc


------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
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Re: JBrowse 1.12.1 installed correctly not loading data

Matt Simenc-2
Sure, here is the trackList.json file.

On Mon, May 9, 2016 at 3:49 PM, Mitchell Graham <[hidden email]> wrote:

Dear Matt,

 

Do you mind sharing your trackList.json file with us? It should not be too large.

 

Thanks,

Mitchell

 

From: Matt Simenc [mailto:[hidden email]]
Sent: Monday, May 09, 2016 6:09 PM
To: [hidden email]
Subject: [Gmod-ajax] JBrowse 1.12.1 installed correctly not loading data

 

Hi, I installed JBrowse 1.12.1 as follows:

 

1. copied to my iMac at /Library/WebServer/Documents/jbrowse

2. ran setup.sh with the following output

 

Joshuas-iMac-2:jbrowse derstudent$ sudo ./setup.sh 

Installing Perl prerequisites ... done.

 

Formatting Volvox example data ... done.

To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

 

Formatting Yeast example data ... done.

To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

 

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

 

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.

 

3. from the directory with index.html I ran prepare-refseq.pl --fasta mygenome.fa. a new directory "data" was created with a tracksList.json file and tracks.conf file

 

4. I pointed Safari at http://localhost/jbrowse/index.html and saw the following screen:

 

Inline image 1

 

5. I clicked the "Volvox test data here" link and JBrowse seems to be working fine with the Volvox data.

 

 

Can anyone help me get my data loaded? I have done everything indicated on the Quick-start Tutorial to get a refseq in a browser and can't find any information on the wikis about this SyntaxError. The file in /Library/WebServer/Documents/jbrowse/data/tracksList.json looks ok to me but I am new to json format.

 

 

Thank you!

Matt Simenc



------------------------------------------------------------------------------
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

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