[Gmod-ajax] Manual Setup

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[Gmod-ajax] Manual Setup

Aaron Spies

Is there a guide that describes how to manually complete the steps that are done by the setup.sh script? We are trying to setup jbrowse in a hosted environment where we do not have access to the server only our site.

 

Thank  you,
Aaron

 

Aaron Spies

Database Administrator Lead

UCF College of Medicine

Office: (407) 266-1239

www.med.ucf.edu

 


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Re: Manual Setup

Scott Cain
Hi Aaron,

I don't know of such a guide, but here's what I'd suggest: set up JBrowse on a server where you do have control.  Use that as a staging server, where you process the data and get it looking the way you want it to look.  When you're happy with it, transfer the whole jbrowse directory to the hosted server, where it will "just work".  When you have updates, do them on the staging server and then rsync to the hosted server (or whatever similar functionality the hosted server provides).

Scott


On Fri, Mar 31, 2017 at 7:59 AM, Aaron Spies <[hidden email]> wrote:

Is there a guide that describes how to manually complete the steps that are done by the setup.sh script? We are trying to setup jbrowse in a hosted environment where we do not have access to the server only our site.

 

Thank  you,
Aaron

 

Aaron Spies

Database Administrator Lead

UCF College of Medicine

Office: <a href="tel:(407)%20266-1239" value="+14072661239" target="_blank">(407) 266-1239

www.med.ucf.edu

 


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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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Re: Manual Setup

Aaron Spies
Hi Scott,
Thank you for the information. We tried this but we are still seeing the welcome message stating that the baseurl has not been configured. I was not sure if the script hardcoded any directory paths or settings that were server specific.

Aaron Spies
Sent via mobile device

On Mar 31, 2017, at 2:22 PM, Scott Cain <[hidden email]> wrote:

Hi Aaron,

I don't know of such a guide, but here's what I'd suggest: set up JBrowse on a server where you do have control.  Use that as a staging server, where you process the data and get it looking the way you want it to look.  When you're happy with it, transfer the whole jbrowse directory to the hosted server, where it will "just work".  When you have updates, do them on the staging server and then rsync to the hosted server (or whatever similar functionality the hosted server provides).

Scott


On Fri, Mar 31, 2017 at 7:59 AM, Aaron Spies <[hidden email]> wrote:

Is there a guide that describes how to manually complete the steps that are done by the setup.sh script? We are trying to setup jbrowse in a hosted environment where we do not have access to the server only our site.

 

Thank  you,
Aaron

 

Aaron Spies

Database Administrator Lead

UCF College of Medicine

Office: <a href="tel:(407)%20266-1239" value="&#43;14072661239" target="_blank"> (407) 266-1239

www.med.ucf.edu

 


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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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Re: Manual Setup

nathandunn

Aaron,

Is there a reason you can’t follow the steps identified in the setup.sh script? 

Are you getting any errors in the javascript console? 

Also, is there a way we could find the configuration file or corresponding directory layout?

Nathan

On Mar 31, 2017, at 5:28 PM, Aaron Spies <[hidden email]> wrote:

Hi Scott,
Thank you for the information. We tried this but we are still seeing the welcome message stating that the baseurl has not been configured. I was not sure if the script hardcoded any directory paths or settings that were server specific.

Aaron Spies
Sent via mobile device

On Mar 31, 2017, at 2:22 PM, Scott Cain <[hidden email]> wrote:

Hi Aaron,

I don't know of such a guide, but here's what I'd suggest: set up JBrowse on a server where you do have control.  Use that as a staging server, where you process the data and get it looking the way you want it to look.  When you're happy with it, transfer the whole jbrowse directory to the hosted server, where it will "just work".  When you have updates, do them on the staging server and then rsync to the hosted server (or whatever similar functionality the hosted server provides).

Scott


On Fri, Mar 31, 2017 at 7:59 AM, Aaron Spies <[hidden email]> wrote:

Is there a guide that describes how to manually complete the steps that are done by the setup.sh script? We are trying to setup jbrowse in a hosted environment where we do not have access to the server only our site.

 

Thank  you,
Aaron

 

Aaron Spies

Database Administrator Lead

UCF College of Medicine

Office: <a href="tel:(407)%20266-1239" value="+14072661239" target="_blank" class=""> (407) 266-1239

www.med.ucf.edu

 


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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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