[Gmod-ajax] Fwd: Jbrowse question

[Ian H. <ihh...@gm...>]

---------- Forwarded message ----------
From: Terry Camerlengo <ter...@gm...>
Date: Mon, Sep 12, 2011 at 5:58 PM
Subject: RE: Jbrowse question
To: mit...@be..., ih...@be...


To the JBrowse team:

I have been trying to get JBrowse included as part of our groups core NGS image.
We are using Solid/Lifescope to generate bam files and so I am working
with the bam-to-json.pl script. I am running Centos 5.6 and the
tutorial works for me (except the bam file part of course). If I run
the bam-to-json script with no params I am getting the help display.
(I assume this means I have all of the library prerequisites.) Then I
run the following...

>>bin/bam-to-json.pl --bam /data/fragmentMapping-1-1.bam (The index file is in the same directory with the same base name)

and I get  the following message:

"Use of uninitialized value in concatenation (.) or string at
bin/bam-to-json.pl line 91."

followed by a Segmentation Fault.

Then I run the following thinking it has something to do with a
missing parameter..

>>bin/bam-to-json.pl --bam /data/fragmentMapping-1-1.bam  --tracklabel bam_simulated --key "Simulated next-gen reads" --cssClass basic --clientConfig '{"featureCss": "background-color: #66F; height: 8px", "histCss": "background-color: #88F"}'

And I just get the Segmentation Fault.

An online search provided nothing useful and I am not sure what the
problem could be. This is a general .bam file used for testing and is
valid. Is there anyway to trouble shoot this? Does JBrowse log error
info someplace? Is there a verbose setting for bam-to-json? Am I
messing up the command line?

Thanks.