Problems Adding a Custom Build

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

Problems Adding a Custom Build

Mackenzie Gavery
Hi,

I am having problems that I think are related:

1.  I have not been able to visualize (in Trackster) a custom build that I recently added (Trackster says: "Could not load chroms for this dbkey:").  In addition, when I try to Operate on Genomic Intervals using bed files associated with that particular build I get an error: Error executing tool: maximum recursion depth exceeded while calling a Python object

2. Now I am trying to add a new custom build to see if there was something wrong with the previous build, and I get an error right after I click on "Add a new Custom Build" in the New Visualization menu  (The error has been logged to our team. If you want to contact us about this error, please reference the following GURU MEDITATION: #9e466e8a843e4ce9be878f3223bb0be4)


I am just wondering if anyone is having similar issues? Or if this is a temporary problem?

Thanks,

Mackenzie

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
|

Re: Problems Adding a Custom Build

Jen Hillman-Jackson
Hello Mackenzie,

Both of these are the same problem. The instructions for how to create and use a Custom reference genome are here:
http://wiki.galaxyproject.org/Support#Custom_reference_genome

My guess is that your reference genome either has format problems or is perhaps comprised of many unassembled/short fragments?

If you want to submit a bug report for the "Operate on Genomic Intervals" job that you ran using this custom reference genome that failed, we can take a closer look.

Best,

Jen
Galaxy team


On 4/24/13 2:30 PM, Mackenzie Gavery wrote:
Hi,

I am having problems that I think are related:

1.  I have not been able to visualize (in Trackster) a custom build that I recently added (Trackster says: "Could not load chroms for this dbkey:").  In addition, when I try to Operate on Genomic Intervals using bed files associated with that particular build I get an error: Error executing tool: maximum recursion depth exceeded while calling a Python object

2. Now I am trying to add a new custom build to see if there was something wrong with the previous build, and I get an error right after I click on "Add a new Custom Build" in the New Visualization menu  (The error has been logged to our team. If you want to contact us about this error, please reference the following GURU MEDITATION: #9e466e8a843e4ce9be878f3223bb0be4)


I am just wondering if anyone is having similar issues? Or if this is a temporary problem?

Thanks,

Mackenzie


___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

-- 
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___________________________________________________________
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/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org