Re: [galaxy-user] problems with MAF alignment file in Galaxy

2014-05-15 Thread Jennifer Jackson 

Hi Amit,

This is occurring when you are uploading a MAF "multizXXway" file 
obtained from UCSC downloads (genome.ucsc.edu) to Galaxy main 
(usegalaxy.org)? Upload using FTP? 
https://wiki.galaxyproject.org/Support#Loading_data


The table browser is generally a poor choice to extract more than a few 
regions with MAF data (per query) as there are limits on how many lines 
of output will be sent over. Incomplete transfers are a common. This 
error could be related to a format or datatype assignment issue from 
that type of issue.


Please give FTP loading a try if you have not already. Then if problems 
continue, you can share a history link with me. Note which dataset was 
the MAF uploaded via FTP. This is how to share: 
https://wiki.galaxyproject.org/Learn/Share


Best,

Jen
Galaxy team

Going forward, please ask questions on our new forum that is replacing 
this list (very soon now):

https://wiki.galaxyproject.org/Support#Biostar

On 5/14/14 10:52 PM, Amit Pande wrote:

Dear Galaxy,

I am trying to import a multiz alignment file for all the insect 
species from the UCSC

genome browser.
Galaxy does not recognize number of blocks in the multiz file as there 
is a question mark in the file format view (? blocks).
Then when I am trying to use the tool ( Extract MAF blocks 
 given a set 
of genomic intervals) then there is an error saying


"An error occurred with this dataset:191757 MAF blocks converted to 
Genomic Intervals for species dm3. There was a problem processing your 
input: exceptions must be old-style classes or derived from 
BaseException, not str" and even when the tool runs it shows the 
following message "

This is a new dataset and not all of its data are available yet "

Please look into the problem.

warm regards,
Amit.


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

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[galaxy-user] problems with MAF alignment file in Galaxy

2014-05-15 Thread Amit Pande 
Dear Galaxy,

I am trying to import a multiz alignment file for all the insect species
from the UCSC
genome browser.
Galaxy does not recognize number of blocks in the multiz file as there is a
question mark in the file format view (? blocks).
Then when I am trying to use the tool ( Extract MAF
blocksgiven a
set of genomic intervals) then there is an error saying

"An error occurred with this dataset:191757 MAF blocks converted to Genomic
Intervals for species dm3. There was a problem processing your input:
exceptions must be old-style classes or derived from BaseException, not
str" and even when the tool runs it shows the following message "
This is a new dataset and not all of its data are available yet "

Please look into the problem.

warm regards,
Amit.
___
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/

Posts to this list will be disabled in May 2014.  In the
meantime, you are encouraged to post all new questions to
Galaxy Biostar.

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:

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