[Gmod-ajax] Docker container for JBrowse

classic Classic list List threaded Threaded
4 messages Options
Reply | Threaded
Open this post in threaded view
|

[Gmod-ajax] Docker container for JBrowse

Andrew Stewart
Hi all,

I've caught a bad case of docker fever and begun "Dockering all the things!".  Anyway, I created a container for JBrowse if anyone is interested in checking it out at https://registry.hub.docker.com/u/andrewcstewart/jbrowse/ .  I looked around but didn't see any existing containers for JBrowse.  Here's how to run it in docker:

docker run -d -p 8080:80 andrewcstewart/jbrowse

Enjoy!

-Andrew

------------------------------------------------------------------------------

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Docker container for JBrowse

Colin
+1 Worked for me! I had to navigate to localhost:8080/JBrowse-1.11.4 though.

Do you have any suggestions on how a someone would run the commands to setup a new genome inside the container :)?

Thanks
-Colin


On Mon, Jul 7, 2014 at 6:23 PM, Andrew Stewart <[hidden email]> wrote:
Hi all,

I've caught a bad case of docker fever and begun "Dockering all the things!".  Anyway, I created a container for JBrowse if anyone is interested in checking it out at https://registry.hub.docker.com/u/andrewcstewart/jbrowse/ .  I looked around but didn't see any existing containers for JBrowse.  Here's how to run it in docker:

docker run -d -p 8080:80 andrewcstewart/jbrowse

Enjoy!

-Andrew

------------------------------------------------------------------------------

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Docker container for JBrowse

Andrew Stewart
Awesome!

There's a couple of ways to do it.  You could start the container in interactive mode, like so:

docker run -i -t -p 8080:80 andrewcstewart/jbrowse /bin/bash

That will drop you into the container, where you can make changes, then ^P^Q to detach.   You can commit those changes as a new image with 'docker commit'.

Another idea is that you could interact with the container outside of it:

docker run -v ./:/data andrewcstewart/jbrowse /path/to/jbrowse/load_track_data.pl /data

I forget the name of the perl script but you get the idea.  That would run the script on local data mounted in the container, and then you'd need to start the web server.

Check out the docs for those commands/options and you should get the basic idea.

On Jul 19, 2014, at 1:17 PM, Colin <[hidden email]> wrote:

+1 Worked for me! I had to navigate to localhost:8080/JBrowse-1.11.4 though.

Do you have any suggestions on how a someone would run the commands to setup a new genome inside the container :)?

Thanks
-Colin


On Mon, Jul 7, 2014 at 6:23 PM, Andrew Stewart <[hidden email]> wrote:
Hi all,

I've caught a bad case of docker fever and begun "Dockering all the things!".  Anyway, I created a container for JBrowse if anyone is interested in checking it out at https://registry.hub.docker.com/u/andrewcstewart/jbrowse/ .  I looked around but didn't see any existing containers for JBrowse.  Here's how to run it in docker:

docker run -d -p 8080:80 andrewcstewart/jbrowse

Enjoy!

-Andrew

------------------------------------------------------------------------------

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax
Reply | Threaded
Open this post in threaded view
|

Re: Docker container for JBrowse

vkrishna
This sounds awesome! This would be perfect for the Arabidopsis Information Portal which is planning to run it’s Science apps (https://www.araport.org/apps) inside Docker containers.
Forwarding this to our portal development team at Texas.

Thank you Andrew.

best,
Vivek

On Jul 19, 2014, at 2:37 PM, Andrew Stewart <[hidden email]> wrote:

Awesome!

There's a couple of ways to do it.  You could start the container in interactive mode, like so:

docker run -i -t -p 8080:80 andrewcstewart/jbrowse /bin/bash

That will drop you into the container, where you can make changes, then ^P^Q to detach.   You can commit those changes as a new image with 'docker commit'.

Another idea is that you could interact with the container outside of it:

docker run -v ./:/data andrewcstewart/jbrowse /path/to/jbrowse/load_track_data.pl /data

I forget the name of the perl script but you get the idea.  That would run the script on local data mounted in the container, and then you'd need to start the web server.

Check out the docs for those commands/options and you should get the basic idea.

On Jul 19, 2014, at 1:17 PM, Colin <[hidden email]> wrote:

+1 Worked for me! I had to navigate to localhost:8080/JBrowse-1.11.4 though.

Do you have any suggestions on how a someone would run the commands to setup a new genome inside the container :)?

Thanks
-Colin


On Mon, Jul 7, 2014 at 6:23 PM, Andrew Stewart <[hidden email]> wrote:
Hi all,

I've caught a bad case of docker fever and begun "Dockering all the things!".  Anyway, I created a container for JBrowse if anyone is interested in checking it out at https://registry.hub.docker.com/u/andrewcstewart/jbrowse/ .  I looked around but didn't see any existing containers for JBrowse.  Here's how to run it in docker:

docker run -d -p 8080:80 andrewcstewart/jbrowse

Enjoy!

-Andrew

------------------------------------------------------------------------------

_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
Want fast and easy access to all the code in your enterprise? Index and
search up to 200,000 lines of code with a free copy of Black Duck
Code Sight - the same software that powers the world's largest code
search on Ohloh, the Black Duck Open Hub! Try it now.
http://p.sf.net/sfu/bds
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax