Thank you very much for solving this Fabien, The PR with your fix has been
created here: https://github.com/galaxyproject/galaxy/pull/1985

Martin

On Mon, Mar 21, 2016 at 5:43 PM fmareuil <fmare...@pasteur.fr> wrote:

> Hi Peter,
>
> 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.
>
> Best,
>
> Fabien
>
>
> --
> Fabien Mareuil | Centre d'Informatique pour la Biologie
> fabien.mare...@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 <fmare...@pasteur.fr>
> <fmare...@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 <fmare...@pasteur.fr>
> <fmare...@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.mare...@pasteur.fr | Institut Pasteur 25,28 rue du Docteur Roux
> 75015
> Paris, France
>
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