Re: JBrowse setup not showing volvox example

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Re: JBrowse setup not showing volvox example

Jocelyn Penington

Actually you can cancel this message. The problem was that I had not followed the instruction to install in a directory accessible to the web browser.

Thank you for your time,

 

Jocelyn

 

From: Jocelyn Penington <[hidden email]>
Date: Friday, 24 February 2017 at 4:08 pm
To: "[hidden email]" <[hidden email]>
Subject: JBrowse setup not showing volvox example

 

Hi,

 

I am trying to install JBrowse.  I have downloaded and unzipped.

JBrowse-1.12.1/docs/tutorial/index.html   opens in my browser (Chrome) OK.

I ran setup.sh at the command line and got the following:

Feb24 14:38 unix306 JBrowse-1.12.1% sh 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Building and installing legacy wiggle format support (superseded by BigWig tracks) ...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Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ...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.

So it looks alright, however, going to the Volvox or yeast sample page gives me a blank page.

The setup.log is attached.

The interesting part seems to be:

“You seem to have neither 'Heap::Simple::XS' nor 'Heap::Simple::Perl' installed.

That should not stop this package from getting installed (in fact, you'll need

to install this package before you can install any of the other two).

However, this package won't be usable until you install one (or both) of these

two.”

 

I will look into installing one of these, but I’m asking for your help in parallel!

Thanks,

Jocelyn

 

-- 

J Sietsma Penington

 

Research Technician

Bioinformatics Division,

Walter and Eliza Hall Institute


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