Re: Regarding GBrowse installation

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Re: Regarding GBrowse installation

Scott Cain
Hi Vijay,

I'm cc'ing the GBrowse mailing list so responses can be archived and other people can provide assistance too.

If when you're installing you get errors, it's not too surprising that you get 500 errors after the installation.  When happened when you installed prerequisites via Synaptic, because I know that there are apt packages for bioperl and biogaphics (and, I think pretty much every GBrowse prereq).  I think you should probably start with trying to solve that.

Scott


On Mon, Jul 11, 2016 at 1:42 PM, Vijay Bhasker <[hidden email]> wrote:
Hi Scott

I am pretty new to GBrowse and my instructor asked me to work on it.I have installed GBrowse using github in Ubuntu and ran perl script "Build.PL" which suggested me to run 1. ./Build test 2. ./Build demo 3. ./Build install. While running the perl script it gives me the errors, Bio::Graphics is not installed and Bio::Root::version is not installed. Also, when I try to open the example databases I come across the 500 internal server error. Could you please help me out how to install Gbrowse and what are the prerequisities to be installed and how to do them because I have installed all the prerequisities in Ubuntu using Synaptic package manager but I guess some of them were missing.So can I have a detailed description of how to follow the installation. Thanks in advance.

Regards
Vijaya Bhasker.

On Sun, Jul 10, 2016 at 10:19 PM, Scott Cain <[hidden email]> wrote:
Hi Vijay,

How wedded are you to GBrowse? It is getting a little old; if you can use it, I'd suggest JBrowse instead. If not, please send  an email to the GBrowse mailing list with a more thorough description of the problem with excerpts of your Apache log files that might shed light on what's going on.

Scott


Sent from my iPhone

> On Jul 10, 2016, at 8:02 PM, Vijay Bhasker <[hidden email]> wrote:
>
> Hi Scott
>
> I am a graduate student from Delaware State University and my majors is in bioinformatics and my research project is installing and adding genome sequence in the GBrowse. I face a lot of errors while going across the tutorial. In the tutorial after adding the features for DNA and 6-frames translation tracks, I am not able to view anything in those tracks. Later when I tried installing it again it shows me other errors which I haven't come across while installing earlier. So, please can you let me know what the error is. Thanks in advance.
>
> Regards
> Vijaya Bhasker.




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Ontario Institute for Cancer Research

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Re: Regarding GBrowse installation

Scott Cain
Hi Vijay,

Please reply all so the GBrowse mailing list will be included.

Have you tried looking for gbrowse in synaptic?  I haven't used it, but with apt-get on the command line you should be able to find it.  I would NOT suggest installing GBrowse via synaptic, since the version would be very old, but I imagine there is a way to install all of the prerequisites without installing GBrowse itself.  If you want to use the command line, I describe how I install on ubuntu with apt-get here:


Scott




On Thu, Jul 14, 2016 at 8:50 AM, Vijay Bhasker <[hidden email]> wrote:
Hi Scott 

I have installed apache2,perl5 , libgd2 , and MySQL server from synaptic . Is there a different way I can install all the prerequisites and after installing the prerequisites which is the best way to install Gbrowse.

Regards
Vijaya Bhasker 



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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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