Hello Luobin,

Galaxy Sample Tracking is not supported by the core Galaxy development team, so 
you're on your own on this one.  I'm told the problem is that the format of the 
library content ID has been changed in the API, so the script needs to be 
updated to reflect that.  Sorry for the inconvenience.

Greg Von Kuster

On Feb 21, 2012, at 4:19 PM, Luobin Yang wrote:

> Hi, Greg,
> I am a bioinformatics research scientist at Idaho State University and we're 
> planning to use the Sample Tracking System for our ION Torrent PGM sequencer. 
> However, I encountered a couple of problems while setting up the Sample 
> Tracking System on our locally installed Galaxy instance. I sent an email to 
> the developer list last week but it seems nobody's interested in it yet. So I 
> am writing to you directly and hope to get some pointers on how to solve the 
> problem.
> So basically I followed the instructions to set up the Sample Tracking System 
> on our system, which is a computer cluster running Ubuntu 10.04 LTS. The 
> problem I have here is transferring the data from the sequencer to the data 
> libraries. So after I clicked the "Transfer" button, the status of data 
> transfer stays on "In queue" forever and the data_transfer.log shows "PUT 
> method not allowed" error. However the sequence files were copied from the 
> sequencer to the folder pointed by library_import_dir. So instead of using 
> Apache as the proxy server, I let Galaxy to provide web services directly.  
> With this change the status of the data transfer changed to "Complete" after 
> the files are copied to the folder pointed by library_import_dir. However, 
> when I browse the data libraries, the data files are not imported to the data 
> library I specified when I submitted the request. And the data_transfer.log 
> has the following error message: 
> "400 Bad Request
> The server could not comply with the request since
> it is either malformed or otherwise incorrect.
> Malformed LibraryFolder id ( 994debf9f6ab02b9912262b0bd04c784 ) specified, 
> unable to decode"
> So I have several questions: 
> 1. Do we need to configure Apache differently so we can still use Apache as 
> the proxy server when using the Sample Tracking System?
> 2. Does the version of RabbitMQ matter for this problem? Because I used the 
> default RabbitMQ version for Utunbu 10.04, which is version 1.7.2 and the 
> latest version of RabbitMQ is 2.7.x. I do not know what versions have you 
> guys tested. 
> 3. Does the folder pointed by library_import_dir related to this problem? On 
> our system library_import_dir points to a folder that's outside the Galaxy 
> installation folder.  
> 4. What python code in Galaxy is related to this issue?
> Thanks,
> Luobin

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to