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
[email protected] <mailto:[email protected]> | 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@HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 and 1:N:0:ATGAGC has been
replaced by a tab.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 <[email protected]>
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 <[email protected]>
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
[email protected] | Institut Pasteur 25,28 rue du Docteur
Roux
75015
Paris, France
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--- lib/galaxy/webapps/galaxy/api/lda_datasets.pyorig 2016-03-21 19:06:53.615038590 +0100
+++ lib/galaxy/webapps/galaxy/api/lda_datasets.py 2016-03-21 18:40:54.519111690 +0100
@@ -404,7 +404,7 @@
"""
if payload:
kwd.update(payload)
- kwd[ 'space_to_tab' ] = 'False'
+ kwd[ 'space_to_tab' ] = False
kwd[ 'to_posix_lines' ] = 'True'
kwd[ 'dbkey' ] = kwd.get( 'dbkey', '?' )
kwd[ 'file_type' ] = kwd.get( 'file_type', 'auto' )
___________________________________________________________
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