I worked on it today and I found the reason of this bug. In the
upload.py tool, the existence of dataset.space_to_tab is tested. In the
old version of the data library, when the option was unchecked, the
value space_to_tab was None and the test worked. But in the new version
the value of space_to_tab is "False", it's a string and the test "if
dataset.space_to_tab" returns True.
It is possible to fix it with a little correction of the
"/lib/galaxy/webapps/galaxy/api/lda_datasets.py".
I join a patch with this email.
I can propose a pull request if you want.
--
Fabien Mareuil | Centre d'Informatique pour la Biologie
fabien.mareuil@pasteur.fr
mailto:fabien.mareuil@pasteur.fr | Institut
Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
On 21/03/2016 09:45, fmareuil wrote:
> Hi Peter,
>
> I tested it on the last version of the dev and master branches.
>
> step-by-step :
> I click on the "shared data/Data Libraries", I select my library and I
> click on the button to upload a file and I select the option "from
> User Directory". I select my fastqsanger file (sequences headers are
> like this :
> @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC
> with a space between @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and
> 1:N:0:ATGAGC and I import it (with or without the auto-detect option).
> When I look the file in a history, the space between
> @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and 1:N:0:ATGAGC has been
> replaced by a tab.
>
> I didn't have this problem with "shared data/ Data Libraries deprecated".
>
> Thank a lot for your help,
> Best,
>
> Fabien
>
> On 18/03/2016 18:59, Peter Cock wrote:
>> 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
fmareuil@pasteur.fr
>> 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
fmareuil@pasteur.fr
>>>> 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.mareuil@pasteur.fr | Institut Pasteur 25,28 rue du Docteur
>>>>> Roux
>>>>> 75015
>>>>> Paris, France
>>>>>
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>