[Gmod-ajax] errors with JBrowse installing

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[Gmod-ajax] errors with JBrowse installing

DataCenter
Dear,
When I exec following command, I got the errors.
 ./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Building and installing legacy wiggle format support (superseded by BigWig tracks) ...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Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... failed.  See setup.log file for error messages. If you really need bam-to-json.pl (most users don't), try reading the Bio-SamTools troubleshooting guide at https://metacpan.org/source/LDS/Bio-SamTools-1.33/README for help getting Bio::DB::Sam installed.

Since I don't need the bam to json support, I ignore these errors. But the IE8.0.7* shows following errors, when to access http://my-server/JBrowse-1.12.1/index.html?data=sample_data/json/volvox

Congratulations, JBrowse is on the web!

However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.

If this is your first time running JBrowse, click here to follow the Quick-start Tutorial to show your data in JBrowse.

However, it appears you have successfully run ./setup.sh, so you can see the Volvox test data here.

Otherwise, please refer to the following resources for help in setting up JBrowse to show your data.

Error message(s):

So what can I do to solve it?

Best wishes!


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Re: errors with JBrowse installing

nathandunn
Did you click on the volvox test data link? 

Nathan

On Nov 3, 2016, at 7:29 PM, DataCenter <[hidden email]> wrote:

Dear,
When I exec following command, I got the errors.
 ./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Building and installing legacy wiggle format support (superseded by BigWig tracks) ...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) ... failed.  See setup.log file for error messages. If you really need bam-to-json.pl (most users don't), try reading the Bio-SamTools troubleshooting guide at https://metacpan.org/source/LDS/Bio-SamTools-1.33/README for help getting Bio::DB::Sam installed.

Since I don't need the bam to json support, I ignore these errors. But the IE8.0.7* shows following errors, when to access http://my-server/JBrowse-1.12.1/index.html?data=sample_data/json/volvox

Congratulations, JBrowse is on the web!

However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.

If this is your first time running JBrowse, click here to follow the Quick-start Tutorial to show your data in JBrowse.

However, it appears you have successfully run ./setup.sh, so you can see the Volvox test data here.

Otherwise, please refer to the following resources for help in setting up JBrowse to show your data.

Error message(s):

So what can I do to solve it?

Best wishes!

<setup.log>
------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
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Re: errors with JBrowse installing

Colin
IE8 probably won't work and probably produces an error similar to "TypeError: Object doesn't support this property or method" (screenshot attached)

It is basically just too old!



-Colin

On Fri, Nov 4, 2016 at 9:20 AM, Lbl <[hidden email]> wrote:
Did you click on the volvox test data link? 

Nathan

On Nov 3, 2016, at 7:29 PM, DataCenter <[hidden email]> wrote:

Dear,
When I exec following command, I got the errors.
 ./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) ... failed.  See setup.log file for error messages. If you really need bam-to-json.pl (most users don't), try reading the Bio-SamTools troubleshooting guide at https://metacpan.org/source/LDS/Bio-SamTools-1.33/README for help getting Bio::DB::Sam installed.

Since I don't need the bam to json support, I ignore these errors. But the IE8.0.7* shows following errors, when to access http://my-server/JBrowse-1.12.1/index.html?data=sample_data/json/volvox

Congratulations, JBrowse is on the web!

However, JBrowse could not start, either because it has not yet been configured and loaded with data, or because of an error.

If this is your first time running JBrowse, click here to follow the Quick-start Tutorial to show your data in JBrowse.

However, it appears you have successfully run ./setup.sh, so you can see the Volvox test data here.

Otherwise, please refer to the following resources for help in setting up JBrowse to show your data.

Error message(s):

So what can I do to solve it?

Best wishes!

<setup.log>
------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Developer Access Program for Intel Xeon Phi Processors
Access to Intel Xeon Phi processor-based developer platforms.
With one year of Intel Parallel Studio XE.
Training and support from Colfax.
Order your platform today. http://sdm.link/xeonphi
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax

win7_ie_8.0.png (37K) Download Attachment