Re: [galaxy-user] Error on custom builds on public galaxy server

2012-02-17 Thread Jennifer Jackson 

Hi Pengfei,

The "User -> Custom Builds:" form is used to set up genomes for use with 
Trackster. To use custom reference genomes with tools from the left tool 
panel, only the fasta dataset in the history is needed. It sounds like 
you already have loaded this, but if not, do this before following the 
steps below, using FTP to load if the genome is large: 
http://wiki.g2.bx.psu.edu/FTPUpload


These are the steps to extract sequences with a custom genome:

1 - starting with the tool "Fetch Sequences -> Extract Genomic DNA"
2 - set "Fetch sequences for intervals in:" to be the BED file of 
coordinates

3 - set "Source for Genomic Data:" to be "History"
4 - the form will refresh to reveal a new menu option, set "Using 
reference file:" to be the dataset from your history that is the fasta 
version of your reference genome

5 - set "Output data type:" to be "FASTA"

It is important that the chromosome/scaffold names in the BED file are 
identical to the identifiers in the FASTA reference genome dataset. If 
there are mismatches, an error will result and corrections to the IDs 
should be made.


Hopefully this helps, but if you continue to have problems, please send 
in a bug report (using the green bug icon) from the red failed Extract 
job and we can provide feedback.


Best,

Jen
Galaxy team

On 2/17/12 8:25 AM, Pengfei Yu wrote:

Hi Jeremy,

Thanks for the help! I can upload fasta data for custom builds
(name:'NCI-H209-hg18'; key:'NCI-H209-V1') now. but when I try to use a
bed file specific for this custom builds to fetch sequences from this
custom genome, it gives error information that no sequences are
available for 'NCI-H209-v1'.
I might do something wrong, do you know what would be the reason?

Thanks!
Pengfei

On Fri, Feb 17, 2012 at 7:40 AM, Jeremy Goecks mailto:jeremy.goe...@emory.edu>> wrote:

Hi Pengfei and Noa,

I suspect this was a temporary problem related to software issues
that we encountered yesterday. Please try again and let us know if
you're still having problems.

Also, note that either a FASTA dataset or a Len file is needed, but
not both. Using a FASTA dataset enables viewing genome data in
Trackster.

Best,
J.


On Feb 17, 2012, at 12:00 AM, Noa Sher wrote:


I also had exactly the same problem yesterday - glad to see that
maybe it wasn't just me.
Happy for help!
Noa

On 16/02/2012 22:24, Pengfei Yu wrote:

Dear sir or madam,

I am using galaxy public server and I am trying to build a custom
genome using the function "custom Builds" in "user" section.
I specified the Name, Key and uploaded the genome fasta file also
the chromosome length file. But when I click "submit", galaxy
gave an error information like that:
""
*Server Error:*
An error occurred. See the error logs for more information. (Turn
debug on to display exception reports here)
""
I don't know where to find the error logs and how to turn debug
on. Could you tell me how to fix the problem and upload the
custom builds?
Thanks a lot!

Pengfei
--
Pengfei Yu
Center of Biophysics and Computational Biology
University of Illinois Urbana-Champaign
Illinois, 61820, US
Cell phone:217-898-6301 



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--
Pengfei Yu
Center of Biophysics and Computational Biology
University of Illinois Urbana-Champaign
Illinois, 61820, US
Cell phone: 217-898-6301



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Re: [galaxy-user] Error on custom builds on public galaxy server

2012-02-17 Thread Pengfei Yu 
Hi Jeremy,

Thanks for the help! I can upload fasta data for custom builds
(name:'NCI-H209-hg18'; key:'NCI-H209-V1') now. but when I try to use a bed
file specific for this custom builds to fetch sequences from this custom
genome, it gives error information that no sequences are available for
'NCI-H209-v1'.
I might do something wrong, do you know what would be the reason?

Thanks!
Pengfei

On Fri, Feb 17, 2012 at 7:40 AM, Jeremy Goecks wrote:

> Hi Pengfei and Noa,
>
> I suspect this was a temporary problem related to software issues that we
> encountered yesterday. Please try again and let us know if you're still
> having problems.
>
> Also, note that either a FASTA dataset or a Len file is needed, but not
> both. Using a FASTA dataset enables viewing genome data in Trackster.
>
> Best,
> J.
>
>
> On Feb 17, 2012, at 12:00 AM, Noa Sher wrote:
>
> I also had exactly the same problem yesterday - glad to see that maybe it
> wasn't just me.
> Happy for help!
> Noa
>
> On 16/02/2012 22:24, Pengfei Yu wrote:
>
> Dear sir or madam,
>
> I am using galaxy public server and I am trying to build a custom genome
> using the function "custom Builds" in "user" section.
> I specified the Name, Key and uploaded the genome fasta file also the
> chromosome length file. But when I click "submit", galaxy gave an error
> information like that:
> ""
> *Server Error:*
> An error occurred. See the error logs for more information. (Turn debug on
> to display exception reports here)
> ""
> I don't know where to find the error logs and how to turn debug on. Could
> you tell me how to fix the problem and upload the custom builds?
> Thanks a lot!
>
> Pengfei
> --
> Pengfei Yu
> Center of Biophysics and Computational Biology
> University of Illinois Urbana-Champaign
> Illinois, 61820, US
> Cell phone: 217-898-6301
>
>
>
> ___
> 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/
>
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> Galaxy analysis and other features on the public server
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>
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>
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>
>
>


-- 
Pengfei Yu
Center of Biophysics and Computational Biology
University of Illinois Urbana-Champaign
Illinois, 61820, US
Cell phone: 217-898-6301
___
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Galaxy analysis and other features on the public server
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using "reply all" in your mail client.  For discussion of
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Re: [galaxy-user] Error on custom builds on public galaxy server

2012-02-17 Thread Jeremy Goecks 
Hi Pengfei and Noa,

I suspect this was a temporary problem related to software issues that we 
encountered yesterday. Please try again and let us know if you're still having 
problems.

Also, note that either a FASTA dataset or a Len file is needed, but not both. 
Using a FASTA dataset enables viewing genome data in Trackster.

Best,
J.


On Feb 17, 2012, at 12:00 AM, Noa Sher wrote:

> I also had exactly the same problem yesterday - glad to see that maybe it 
> wasn't just me.
> Happy for help!
> Noa
> 
> On 16/02/2012 22:24, Pengfei Yu wrote:
>> 
>> Dear sir or madam,
>> 
>> I am using galaxy public server and I am trying to build a custom genome 
>> using the function "custom Builds" in "user" section. 
>> I specified the Name, Key and uploaded the genome fasta file also the 
>> chromosome length file. But when I click "submit", galaxy gave an error 
>> information like that:
>> ""
>> Server Error:
>> An error occurred. See the error logs for more information. (Turn debug on 
>> to display exception reports here) 
>> ""
>> I don't know where to find the error logs and how to turn debug on. Could 
>> you tell me how to fix the problem and upload the custom builds?
>> Thanks a lot!
>> 
>> Pengfei
>> -- 
>> Pengfei Yu 
>> Center of Biophysics and Computational Biology
>> University of Illinois Urbana-Champaign
>> Illinois, 61820, US
>> Cell phone: 217-898-6301
>> 
>> 
>> 
>> ___
>> 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.  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/

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Re: [galaxy-user] Error on custom builds on public galaxy server

2012-02-17 Thread Jennifer Jackson 

Hello Pengfei, Noa,

Galaxy was experiencing intermittent cluster failures yesterday. Please 
run your jobs again. I was able to create a test build a few minutes ago 
without a problem at the public Main instance.


We are very sorry for the inconvenience,

Jen
Galaxy team


On 2/16/12 12:24 PM, Pengfei Yu wrote:

Dear sir or madam,

I am using galaxy public server and I am trying to build a custom genome
using the function "custom Builds" in "user" section.
I specified the Name, Key and uploaded the genome fasta file also the
chromosome length file. But when I click "submit", galaxy gave an error
information like that:
""
*Server Error:*
An error occurred. See the error logs for more information. (Turn debug
on to display exception reports here)
""
I don't know where to find the error logs and how to turn debug on.
Could you tell me how to fix the problem and upload the custom builds?
Thanks a lot!

Pengfei
--
Pengfei Yu
Center of Biophysics and Computational Biology
University of Illinois Urbana-Champaign
Illinois, 61820, US
Cell phone: 217-898-6301 



___
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

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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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Re: [galaxy-user] Error on custom builds on public galaxy server

2012-02-17 Thread Pengfei Yu 
Yeah, Hope we could find the answer from Galaxy team soon :-)

Pengfei

On Thu, Feb 16, 2012 at 11:00 PM, Noa Sher  wrote:

>  I also had exactly the same problem yesterday - glad to see that maybe
> it wasn't just me.
>
> Happy for help!
>
> Noa
>
> On 16/02/2012 22:24, Pengfei Yu wrote:
>
> Dear sir or madam,
>
>  I am using galaxy public server and I am trying to build a custom genome
> using the function "custom Builds" in "user" section.
> I specified the Name, Key and uploaded the genome fasta file also the
> chromosome length file. But when I click "submit", galaxy gave an error
> information like that:
> ""
> *Server Error:*
> An error occurred. See the error logs for more information. (Turn debug on
> to display exception reports here)
> ""
>  I don't know where to find the error logs and how to turn debug on.
> Could you tell me how to fix the problem and upload the custom builds?
> Thanks a lot!
>
>  Pengfei
> --
> Pengfei Yu
> Center of Biophysics and Computational Biology
> University of Illinois Urbana-Champaign
> Illinois, 61820, US
> Cell phone: 217-898-6301
>
>
>
> ___
> 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/
>
>


-- 
Pengfei Yu
Center of Biophysics and Computational Biology
University of Illinois Urbana-Champaign
Illinois, 61820, US
Cell phone: 217-898-6301
___
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Re: [galaxy-user] Error on custom builds on public galaxy server

2012-02-16 Thread Noa Sher 

  
  
I also had exactly the same problem yesterday - glad to see that
  maybe it wasn't just me.
Happy for help!
Noa


On 16/02/2012 22:24, Pengfei Yu wrote:
Dear sir or madam,
  
  
  I am using galaxy public server and I am trying to build a
custom genome using the function "custom Builds" in "user"
section. 
  I specified the Name, Key and uploaded the genome fasta file
also the chromosome length file. But when I click "submit",
galaxy gave an error information like that:
  ""
  Server
Error:
  An
  error occurred. See the error logs for more information. (Turn
  debug on to display exception reports here) 
  ""

I don't know where to find the error logs and how to turn
  debug on. Could you tell me how to fix the problem and upload
  the custom builds?
Thanks a lot!


Pengfei
-- 
Pengfei Yu 
Center of Biophysics and Computational Biology
University of Illinois Urbana-Champaign
Illinois, 61820, US
Cell phone: 217-898-6301

  
  
  
  
  ___
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