Re: [galaxy-user] CloudMan Web Launcher / BioCloudCentral - Not showing public DNS

2012-01-27 Thread mailing list
Hmm, I just launched again (I had Firebug enabled and JS started
paused).  When I unpaused it worked.

It's looking more and more like it's making a call to the GET URL too
quickly and getting back some kind of bad value that's throwing off
the javascript logic?  Undefined?   That's my best guess at this
point.

-Greg


On Fri, Jan 27, 2012 at 7:51 AM, mailing list margeem...@gmail.com wrote:
 Hi Brad,

 I tried again just now.

 I launched and left it alone for 5 minutes.  It said not available
 in the Instance State cell.  And nothing else happened.

 Then I ran this in Firebug and it did fill in the proper information
 on the page:
 update_instance_state();
 GET http://biocloudcentral.herokuapp.com/state
 200 OK
                171ms
 undefined
 running

 I'm not sure where that undefined is coming from.  Maybe that is
 part of the problem?  It seems like update_instance_state() isn't
 being run.

 I don't have anything blocking JS.

 Here's my system/browser info:

 Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.6; en-US; rv:1.9.2.25)
 Gecko/20111212 Firefox/3.6.25

 By the way, it might be a nice touch to put loading icons next to the
 cells in the table that will get updated.  There are some here:
 http://www.ajaxload.info/
 The Javascript function could just remove or hide the icons once the
 final info is loaded.

 -Greg



 On Thu, Jan 26, 2012 at 9:03 PM, Brad Chapman chapm...@50mail.com wrote:

 Greg;
 As you dug into, the javascript function should keep refreshing and
 checking the state until the information is available from the EC2
 console, and then fill it in. This does work for me as intended on
 Firefox 9.0.1 and Chrome. It normally takes a minute or so for the
 server information to be available from Amazon.

 Are you seeing the failure to refresh and fill in the information every
 time you use BioCloudCentral or intermittently? Do you have any
 javascript blockers or other magic running? Anything else that might
 help with reproducing this?

 Thanks for letting us know about the problem and hopefully we can get it
 sorted out,
 Brad

 Ok, I did some more investigating.

 After I launched (5 minutes later if it matters), I opened up Firebug
 and ran update_instance_state(); and it did fill in the information.

 Maybe there's something wrong in the JS logic?  Is it setting the
 state to running before it has the information?

 Here's the javascript for easy reference:

   script
     function update_instance_state() {
         $.get(/state,
             function(data) {
                 console.log(data.instance_state);
                 if (data.instance_state != '') {
                     $('#inst_state').html(data.instance_state);
                 }
                 if (data.instance_state != 'running') {

 window.setTimeout(function(){update_instance_state()}, 5000);
                 } else {
                   $('#ssh_public_dns').html(data.public_dns);
                   $('#nx_public_dns').html(data.public_dns);
                   $('#cloud_url').html('a href=http://' +
                      data.public_dns + '/cloud target=_blank' +
                      data.public_dns + '/a');
                 }
             });
     }
     $(document).ready(function() {
         update_instance_state();
     });
   /script


 Thanks,

 Greg


 On Thu, Jan 26, 2012 at 11:04 AM, mailing list margeem...@gmail.com wrote:
  Hi guys,
 
  When I launch using BioCloudCentral
  (http://biocloudcentral.herokuapp.com) I noticed it doesn't show my
  public DNS.  Even if I wait for a few minutes.
 
  For the Public IP (Cloudman Console) table cell, it just shows
  blank, and for the SSH access area is just says ssh ubuntu@
 
  It hasn't been a big deal because I just pull it from my EC2 console.
  But now I'm writing up some documentation for other researchers to use
  our application running on CloudMan, and it adds a lot of complexity
  to the documentation to tell them to log into the EC2 console, click
  on instances, copy the public DNS ...  It would be excellent if they
  could just click a link from the launch page!
 
  Let me know if I can help with debugging.
 
  Thanks again,
 
  Greg

 ___
 The Galaxy User list should be used for the discussion of
 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

 To manage your subscriptions to this and other Galaxy lists,
 please use the interface at:

   http://lists.bx.psu.edu/

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  

[galaxy-user] Obtaining Mouse-projected alignments from Galaxy?

2012-01-27 Thread Paralkar, Vikram
Hello,

In the Fetch Alignments section, it's currently possible to get only
human-projected alignments (from 46-way multiZ (hg19) MAFs). Any way you
could add the ability to choose mouse-projected alignments? I tried to do
this by downloading the multiz30way (mm9) MAFs from the UCSC browser to my
history and using it as the Alignment from your history, but then I can't
choose specific species from the 30 species list.

Any way you could add the ability to choose mouse-projected MAFs, and then
choose specific species from it, just the way you currently have for
human-projection. Thanks.

Vikram



The information contained in this e-mail message is intended only for the 
personal and confidential use of the recipient(s) named above. If the reader of 
this message is not the intended recipient or an agent responsible for 
delivering it to the intended recipient, you are hereby notified that you have 
received this document in error and that any review, dissemination, 
distribution, or copying of this message is strictly prohibited. If you have 
received this communication in error, please notify us immediately by e-mail, 
and delete the original message.
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/


[galaxy-user] January 27, 2012 Galaxy Distribution News Brief

2012-01-27 Thread Jennifer Jackson

January 27, 2012 Galaxy Distribution   News Brief


Complete News Brief
* http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_01_27


Highlights:

* Important metadata and Python 2.5 support corrections
* SAMtools upgraded for version 0.1.18. Mpileup added.
* Dynamic filtering, easy color options, and quicker
  indexing enhance Trackster
* Set up your Galaxy instance to run cluster jobs as
  the real user, not the Galaxy owner
* Improvements to metadata handling and searching in
  the Tool Shed
* Improved solutions for schema access, jobs management,
   workflow imports and inputs.
* New datatypes (Eland, XML), multiple tool enhancements,
  and bug fixes.


Get Galaxy!
* http://getgalaxy.org

new: % hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: % hg pull -u -r 26920e20157f


Read the release announcement and see the prior release history
* http://wiki.g2.bx.psu.edu/DevNewsBriefs/


Need help with a local instance?

Search with our custom google tools!
* http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching

And consider subscribing to the galaxy-dev mailing list!
* http://wiki.g2.bx.psu.edu/Mailing%20Lists#Subscribing_and_Unsubscribing




--
Jennifer Jackson
Galaxy Team

http://usegalaxy.org
http://galaxyproject.org
http://galaxyproject.org/wiki/Support



___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/