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

Thank :)! Fabien Le 23/03/2016 00:01, Martin Čech a écrit : Thank you for all the help Peter! Also this is already backported and fixed in 16.01 Sorry for causing this bug in the first place. M. On Tue, Mar 22, 2016, 18:29 Peter Cock > wrote: Well done

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

Thank you for all the help Peter! Also this is already backported and fixed in 16.01 Sorry for causing this bug in the first place. M. On Tue, Mar 22, 2016, 18:29 Peter Cock wrote: > Well done for solving this Fabien, with only a small hint from me. > I'm glad to see your suggested fix has alr

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

Well done for solving this Fabien, with only a small hint from me. I'm glad to see your suggested fix has already been applied to the Galaxy repository so should be in the next stable release. Thank you! Peter (Also thank you Martin, Nicola, Dan, etc) On Tue, Mar 22, 2016 at 8:43 PM, Martin Če

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

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 wrote: > Hi Peter, > > I worked on it today and I found the reason of this bug. In the upload.py > tool, th

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

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 va

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

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 ar

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

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:

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

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

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

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

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

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