(some) Tabular files not displaying correctly

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(some) Tabular files not displaying correctly

Lukasse, Pieter

Hi ,

 

I have this strange thing on my Galaxy server where some tabular files display correctly in the central frame while others will just display as some kind of plain text file where the tabs are read as spaces...but when loading them in excel they work just fine!

 

Has anyone seen this before and what would be the solution/workaround?

 

Screenshots:

 

 

Bad:

 

Good:

 

 

 

 

Thanks and regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

+31-317481122; skype: pieter.lukasse.wur

http://www.pri.wur.nl

 


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(some) Tabular files not displaying correctly

Lukasse, Pieter

Hi ,

 

I have this strange thing on my Galaxy server where some tabular files display correctly in the central frame while others will just display as some kind of plain text file where the tabs are read as spaces...but when loading them in excel they work just fine!

 

Has anyone seen this before and what would be the solution/workaround?

 

Screenshots:

 

 

Bad:

 

Good:

 

 

 

 

Thanks and regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

+31-317481122; skype: pieter.lukasse.wur

http://www.pri.wur.nl

 


___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

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Re: (some) Tabular files not displaying correctly

Lukasse, Pieter
In reply to this post by Lukasse, Pieter

Hi, I just tested this on a recent version of Galaxy (last week) and it is still the case...am I the only one facing this?

 

Regards,

 

Pieter

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Lukasse, Pieter
Sent: donderdag 6 maart 2014 11:50
To: [hidden email]
Subject: [galaxy-dev] (some) Tabular files not displaying correctly

 

Hi ,

 

I have this strange thing on my Galaxy server where some tabular files display correctly in the central frame while others will just display as some kind of plain text file where the tabs are read as spaces...but when loading them in excel they work just fine!

 

Has anyone seen this before and what would be the solution/workaround?

 

Screenshots:

 

 

Bad:

 

Good:

 

 

 

 

Thanks and regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

+31-317481122; skype: pieter.lukasse.wur

http://www.pri.wur.nl

 


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: (some) Tabular files not displaying correctly

Dannon Baker-2
Hey Pieter,

I have not seen this myself.  Could you share a file that reproduces this issue with me?

-Dannon


On Tue, Mar 25, 2014 at 11:25 AM, Lukasse, Pieter <[hidden email]> wrote:

Hi, I just tested this on a recent version of Galaxy (last week) and it is still the case...am I the only one facing this?

 

Regards,

 

Pieter

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Lukasse, Pieter
Sent: donderdag 6 maart 2014 11:50
To: [hidden email]
Subject: [galaxy-dev] (some) Tabular files not displaying correctly

 

Hi ,

 

I have this strange thing on my Galaxy server where some tabular files display correctly in the central frame while others will just display as some kind of plain text file where the tabs are read as spaces...but when loading them in excel they work just fine!

 

Has anyone seen this before and what would be the solution/workaround?

 

Screenshots:

 

 

Bad:

 

Good:

 

 

 

 

Thanks and regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

<a href="tel:%2B31-317481122" value="+31317481122" target="_blank">+31-317481122; skype: pieter.lukasse.wur

http://www.pri.wur.nl

 


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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:
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Re: (some) Tabular files not displaying correctly

Carl Eberhard
In reply to this post by Lukasse, Pieter
Hello, Pieter

How many columns does the dataset in the original mail have? It looks like quite a few.

I know that other users have had issues with tabular data that had a large number of columns.

Does the error occur with any formats or files that have less than 20 columns?

Thanks,
Carl


On Tue, Mar 25, 2014 at 11:25 AM, Lukasse, Pieter <[hidden email]> wrote:

Hi, I just tested this on a recent version of Galaxy (last week) and it is still the case...am I the only one facing this?

 

Regards,

 

Pieter

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Lukasse, Pieter
Sent: donderdag 6 maart 2014 11:50
To: [hidden email]
Subject: [galaxy-dev] (some) Tabular files not displaying correctly

 

Hi ,

 

I have this strange thing on my Galaxy server where some tabular files display correctly in the central frame while others will just display as some kind of plain text file where the tabs are read as spaces...but when loading them in excel they work just fine!

 

Has anyone seen this before and what would be the solution/workaround?

 

Screenshots:

 

 

Bad:

 

Good:

 

 

 

 

Thanks and regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

<a href="tel:%2B31-317481122" value="+31317481122" target="_blank">+31-317481122; skype: pieter.lukasse.wur

http://www.pri.wur.nl

 


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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Re: (some) Tabular files not displaying correctly

Lukasse, Pieter

Hi Carl, Dannon,

 

It has 89 columns ;) . Indeed if I reduce the number of columns to 18, then displays correctly.

 

I’m sending a simple example attached which you can use to reproduce the problem.

 

Thanks for your help.

 

Best regards,

 

Pieter.

 

From: Carl Eberhard [mailto:[hidden email]]
Sent: woensdag 26 maart 2014 14:05
To: Lukasse, Pieter
Cc: [hidden email]
Subject: Re: [galaxy-dev] (some) Tabular files not displaying correctly

 

Hello, Pieter

 

How many columns does the dataset in the original mail have? It looks like quite a few.

 

I know that other users have had issues with tabular data that had a large number of columns.

 

Does the error occur with any formats or files that have less than 20 columns?

 

Thanks,

Carl

 

On Tue, Mar 25, 2014 at 11:25 AM, Lukasse, Pieter <[hidden email]> wrote:

Hi, I just tested this on a recent version of Galaxy (last week) and it is still the case...am I the only one facing this?

 

Regards,

 

Pieter

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Lukasse, Pieter
Sent: donderdag 6 maart 2014 11:50
To: [hidden email]
Subject: [galaxy-dev] (some) Tabular files not displaying correctly

 

Hi ,

 

I have this strange thing on my Galaxy server where some tabular files display correctly in the central frame while others will just display as some kind of plain text file where the tabs are read as spaces...but when loading them in excel they work just fine!

 

Has anyone seen this before and what would be the solution/workaround?

 

Screenshots:

 

 

Bad:

 

Good:

 

 

 

 

Thanks and regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

<a href="tel:%2B31-317481122" target="_blank">+31-317481122; skype: pieter.lukasse.wur

http://www.pri.wur.nl

 


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

 


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
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Galaxy1-[METEXP_-_Query_Database__on_data_16]-.tabular (5K) Download Attachment
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Re: (some) Tabular files not displaying correctly

Dannon Baker-2
That makes sense, then.  Because of problems we'd run into rendering very wide datasets (larger than this), the incremental tabular display is limited to 50 columns on the galaxy side.  89 columns should probably still work just fine.  If you want to tweak your local instance to change this behavior, see lib/galaxy/datatypes/tabular.py, line 284 or so (https://bitbucket.org/galaxy/galaxy-central/src/37fa3f5a47f8fc45755ac1ca758a852bb76ea999/lib/galaxy/datatypes/tabular.py?at=default#cl-284) to change it.


On Fri, Mar 28, 2014 at 8:57 AM, Lukasse, Pieter <[hidden email]> wrote:

Hi Carl, Dannon,

 

It has 89 columns ;) . Indeed if I reduce the number of columns to 18, then displays correctly.

 

I’m sending a simple example attached which you can use to reproduce the problem.

 

Thanks for your help.

 

Best regards,

 

Pieter.

 

From: Carl Eberhard [mailto:[hidden email]]
Sent: woensdag 26 maart 2014 14:05
To: Lukasse, Pieter
Cc: [hidden email]
Subject: Re: [galaxy-dev] (some) Tabular files not displaying correctly

 

Hello, Pieter

 

How many columns does the dataset in the original mail have? It looks like quite a few.

 

I know that other users have had issues with tabular data that had a large number of columns.

 

Does the error occur with any formats or files that have less than 20 columns?

 

Thanks,

Carl

 

On Tue, Mar 25, 2014 at 11:25 AM, Lukasse, Pieter <[hidden email]> wrote:

Hi, I just tested this on a recent version of Galaxy (last week) and it is still the case...am I the only one facing this?

 

Regards,

 

Pieter

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Lukasse, Pieter
Sent: donderdag 6 maart 2014 11:50
To: [hidden email]
Subject: [galaxy-dev] (some) Tabular files not displaying correctly

 

Hi ,

 

I have this strange thing on my Galaxy server where some tabular files display correctly in the central frame while others will just display as some kind of plain text file where the tabs are read as spaces...but when loading them in excel they work just fine!

 

Has anyone seen this before and what would be the solution/workaround?

 

Screenshots:

 

 

Bad:

 

Good:

 

 

 

 

Thanks and regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

<a href="tel:%2B31-317481122" target="_blank">+31-317481122; skype: pieter.lukasse.wur

http://www.pri.wur.nl

 


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

 



___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: (some) Tabular files not displaying correctly

Lukasse, Pieter

Thanks Dannon,

 

I see a “matrix” display is planned. Looking forward to that ;)

 

What kind of problems can I expect if I increase the limit?

 

Thanks and regards ,

 

Pieter.

 

From: Dannon Baker [mailto:[hidden email]]
Sent: vrijdag 28 maart 2014 14:28
To: Lukasse, Pieter
Cc: Carl Eberhard; [hidden email]
Subject: Re: [galaxy-dev] (some) Tabular files not displaying correctly

 

That makes sense, then.  Because of problems we'd run into rendering very wide datasets (larger than this), the incremental tabular display is limited to 50 columns on the galaxy side.  89 columns should probably still work just fine.  If you want to tweak your local instance to change this behavior, see lib/galaxy/datatypes/tabular.py, line 284 or so (https://bitbucket.org/galaxy/galaxy-central/src/37fa3f5a47f8fc45755ac1ca758a852bb76ea999/lib/galaxy/datatypes/tabular.py?at=default#cl-284) to change it.

 

On Fri, Mar 28, 2014 at 8:57 AM, Lukasse, Pieter <[hidden email]> wrote:

Hi Carl, Dannon,

 

It has 89 columns ;) . Indeed if I reduce the number of columns to 18, then displays correctly.

 

I’m sending a simple example attached which you can use to reproduce the problem.

 

Thanks for your help.

 

Best regards,

 

Pieter.

 

From: Carl Eberhard [mailto:[hidden email]]
Sent: woensdag 26 maart 2014 14:05
To: Lukasse, Pieter
Cc: [hidden email]
Subject: Re: [galaxy-dev] (some) Tabular files not displaying correctly

 

Hello, Pieter

 

How many columns does the dataset in the original mail have? It looks like quite a few.

 

I know that other users have had issues with tabular data that had a large number of columns.

 

Does the error occur with any formats or files that have less than 20 columns?

 

Thanks,

Carl

 

On Tue, Mar 25, 2014 at 11:25 AM, Lukasse, Pieter <[hidden email]> wrote:

Hi, I just tested this on a recent version of Galaxy (last week) and it is still the case...am I the only one facing this?

 

Regards,

 

Pieter

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Lukasse, Pieter
Sent: donderdag 6 maart 2014 11:50
To: [hidden email]
Subject: [galaxy-dev] (some) Tabular files not displaying correctly

 

Hi ,

 

I have this strange thing on my Galaxy server where some tabular files display correctly in the central frame while others will just display as some kind of plain text file where the tabs are read as spaces...but when loading them in excel they work just fine!

 

Has anyone seen this before and what would be the solution/workaround?

 

Screenshots:

 

 

Bad:

 

Good:

 

 

 

 

Thanks and regards,

 

Pieter Lukasse

Wageningen UR, Plant Research International

Departments of Bioscience and Bioinformatics

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
Wageningen, the Netherlands

<a href="tel:%2B31-317481122" target="_blank">+31-317481122; skype: pieter.lukasse.wur

http://www.pri.wur.nl

 


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

 

 


___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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