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
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(a)pasteur.fr <mailto:firstname.lastname@example.org> | Institut
25,28 rue du Docteur Roux 75015 Paris, France
On 21/03/2016 09:45, fmareuil wrote:
I tested it on the last version of the dev and master branches.
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 :
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@HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and 1:N:0:ATGAGC has been
replaced by a tab.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,
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.
> On Fri, Mar 18, 2016 at 5:34 PM, Fabien Mareuil <fmareuil(a)pasteur.fr>
>> Hi Peter,
>> Thank a lot for this information, I didn't found this option for the
>> 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.
>> 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.
>>> On Fri, Mar 18, 2016 at 3:26 PM, Fabien Mareuil <fmareuil(a)pasteur.fr>
>>>> 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
>>>> because it doesn't work with tab character. With the direct upload
>>>> the deprecated version of Data Libraries no tab character is
>>>> added. Do
>>>> have some idea to correct this problem? Thanks a lot Best regards --
>>>> Fabien Mareuil | Centre d'Informatique pour la Biologie
>>>> fabien.mareuil(a)pasteur.fr | Institut Pasteur 25,28 rue du Docteur
>>>> Paris, France
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