Re: [galaxy-dev] automatic adding of a tab in a fastq header

2016-03-18 Thread Peter Cock 
Can you provide more details - in particular the version of Galaxy you
are running? A step-by-step description of how you did the data import
might be useful too for the Galaxy team to try to reproduce this.

Peter

On Fri, Mar 18, 2016 at 5:34 PM, Fabien Mareuil  wrote:
> Hi Peter,
>
> Thank a lot for this information, I didn't found this option for the new
> version of the Data Libraries.
> This could explain why there is this conversion.
> I tested it with an automatic format detection and when I set explicitly the
> format but in the two cases a tab was added.
>
> Fabien
>
>
> Le 18/03/2016 17:04, Peter Cock a écrit :
>>
>> Hi Fabien,
>>
>> There is a Galaxy upload option to turn spaces into tabs, useful for
>> tables of data. Is that being ticked by mistake? That would explain
>> this problem.
>>
>> Also I would check if the FASTQ file format is being detected
>> automatically, or set explicitly (e.g. fastqsanger)? Doing that ought
>> to prevent any changes.
>>
>> Peter
>>
>> On Fri, Mar 18, 2016 at 3:26 PM, Fabien Mareuil 
>> wrote:
>>>
>>> Hi,
>>>
>>> We got a problem with the new version of Data libraries. When we upload a
>>> fastq file from a User Directory, a tabulation character is added in the
>>> header in replacement of a space character.
>>>
>>> from @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC to
>>> @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965  1:N:0:ATGAGC
>>>
>>>
>>> This behavior causes an error with cutadapt 1.6 (maybe with other tools)
>>> because it doesn't work with tab character. With the direct upload tool
>>> or
>>> the deprecated version of Data Libraries no tab character is added. Do
>>> you
>>> have some idea to correct this problem? Thanks a lot Best regards --
>>> Fabien Mareuil | Centre d'Informatique pour la Biologie
>>> fabien.mare...@pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux
>>> 75015
>>> Paris, France
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
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>>> and other Galaxy lists, please use the interface at:
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>>>
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>>>http://galaxyproject.org/search/mailinglists/
>
>
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[galaxy-dev] planemo update failing on testtoolshed

2016-03-18 Thread Peter van Heusden 
Hi there

I'm trying to update a newly created tool on the test tool shed and I get
this error:

$ planemo shed_update -t testtoolshed
cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git rev-parse HEAD
cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git diff --quiet
Could not update split_fasta_chunks
Unexpected response from galaxy: 500: 
  Internal Server Error
  
Internal Server Error
The server has either erred or is incapable of performing
the requested operation.




WSGI Server
  


Repository metadata updated.
Failed to update a repository.

I might have accidentally created a "bad" repository that is leading to
this error. This is with version 0.23.0. Alternately, is there a way to
delete the tool so that I can try and recreate it?

Thanks!
Peter
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Re: [galaxy-dev] automatic adding of a tab in a fastq header

2016-03-18 Thread Fabien Mareuil 

Hi Peter,

Thank a lot for this information, I didn't found this option for the new 
version of the Data Libraries.

This could explain why there is this conversion.
I tested it with an automatic format detection and when I set explicitly 
the format but in the two cases a tab was added.


Fabien

Le 18/03/2016 17:04, Peter Cock a écrit :

Hi Fabien,

There is a Galaxy upload option to turn spaces into tabs, useful for
tables of data. Is that being ticked by mistake? That would explain
this problem.

Also I would check if the FASTQ file format is being detected
automatically, or set explicitly (e.g. fastqsanger)? Doing that ought
to prevent any changes.

Peter

On Fri, Mar 18, 2016 at 3:26 PM, Fabien Mareuil  wrote:

Hi,

We got a problem with the new version of Data libraries. When we upload a
fastq file from a User Directory, a tabulation character is added in the
header in replacement of a space character.

from @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC to
@HWI-D00395:188:HYGNFADXX:2:1108:1315:1965  1:N:0:ATGAGC


This behavior causes an error with cutadapt 1.6 (maybe with other tools)
because it doesn't work with tab character. With the direct upload tool or
the deprecated version of Data Libraries no tab character is added. Do you
have some idea to correct this problem? Thanks a lot Best regards --
Fabien Mareuil | Centre d'Informatique pour la Biologie
fabien.mare...@pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux 75015
Paris, France

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Re: [galaxy-dev] automatic adding of a tab in a fastq header

2016-03-18 Thread Peter Cock 
Hi Fabien,

There is a Galaxy upload option to turn spaces into tabs, useful for
tables of data. Is that being ticked by mistake? That would explain
this problem.

Also I would check if the FASTQ file format is being detected
automatically, or set explicitly (e.g. fastqsanger)? Doing that ought
to prevent any changes.

Peter

On Fri, Mar 18, 2016 at 3:26 PM, Fabien Mareuil  wrote:
> Hi,
>
> We got a problem with the new version of Data libraries. When we upload a
> fastq file from a User Directory, a tabulation character is added in the
> header in replacement of a space character.
>
> from @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC to
> @HWI-D00395:188:HYGNFADXX:2:1108:1315:19651:N:0:ATGAGC
>
>
> This behavior causes an error with cutadapt 1.6 (maybe with other tools)
> because it doesn't work with tab character. With the direct upload tool or
> the deprecated version of Data Libraries no tab character is added. Do you
> have some idea to correct this problem? Thanks a lot Best regards --
> Fabien Mareuil | Centre d'Informatique pour la Biologie
> fabien.mare...@pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux 75015
> Paris, France
>
> ___
> 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:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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