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: [cid:image001.jpg@01CF3948.EA0F8D30]

Good:

[cid:image004.jpg@01CF3948.EA0F8D30]

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.nlhttp://www.pri.wur.nl/

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 pieter.lukasse@wur.nlwrote:

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:* galaxy-dev-bounces@lists.bx.psu.edu [mailto: galaxy-dev-bounces@lists.bx.psu.edu] *On Behalf Of *Lukasse, Pieter *Sent:* donderdag 6 maart 2014 11:50 *To:* galaxy-dev@lists.bx.psu.edu *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

---

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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:carlfeberhard@gmail.com] Sent: woensdag 26 maart 2014 14:05 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edu 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 <pieter.lukasse@wur.nlmailto:pieter.lukasse@wur.nl> 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: galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: donderdag 6 maart 2014 11:50 To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 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: [cid:image001.jpg@01CF4A8C.C6668C80]

Good:

[cid:image002.jpg@01CF4A8C.C6668C80]

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 +31-317481122tel:%2B31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://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/

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:dannon.baker@gmail.com] Sent: vrijdag 28 maart 2014 14:28 To: Lukasse, Pieter Cc: Carl Eberhard; galaxy-dev@lists.bx.psu.edu 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/37fa3f5a47f8fc45755ac1ca758a...) to change it.

On Fri, Mar 28, 2014 at 8:57 AM, Lukasse, Pieter <pieter.lukasse@wur.nlmailto:pieter.lukasse@wur.nl> 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:carlfeberhard@gmail.commailto:carlfeberhard@gmail.com] Sent: woensdag 26 maart 2014 14:05 To: Lukasse, Pieter Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 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 <pieter.lukasse@wur.nlmailto:pieter.lukasse@wur.nl> 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: galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edumailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Lukasse, Pieter Sent: donderdag 6 maart 2014 11:50 To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu 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: [cid:image001.jpg@01CF4FF3.88E85B10]

Good:

[cid:image002.jpg@01CF4FF3.88E85B10]

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 +31-317481122tel:%2B31-317481122; skype: pieter.lukasse.wur http://www.pri.wur.nlhttp://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/