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

[Fabien Mareuil]

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 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 Čech mailto:mar...@bx.psu.edu>> wrote:
> 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 mailto: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
>>



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

[Martin Čech]

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 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 Čech  wrote:
> > 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, 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
> >>
>
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Re: [galaxy-dev] automatic adding of a tab in a fastq header

[Peter Cock]

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 Čech  wrote:
> 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, 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
>>
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Re: [galaxy-dev] automatic adding of a tab in a fastq header

[Martin Čech]

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, 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 
>  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 
> 
> 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
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
>
>
>
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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Re: [galaxy-dev] automatic adding of a tab in a fastq header

[fmareuil]

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

[fmareuil]

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

[Fabien Mareuil]

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

[Peter Cock]

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 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 
>> 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
>>>
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>>https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>http://galaxyproject.org/search/mailinglists/
>
>
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Re: [galaxy-dev] automatic adding of a tab in a fastq header

[Fabien Mareuil]

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

[Peter Cock]

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  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:2:1108:1315:19651: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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