problem with latest toolshed devteam cuffmerge wrapper multi-select

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problem with latest toolshed devteam cuffmerge wrapper multi-select

Nikhil Joshi-2
Hi all,

We run our own custom galaxy instance in the Amazon Cloud and I am updating our instance with the latest toolshed files. For cuffmerge, in past revisions, we would just have a button to add another GTF input. However, this latest one (10:b6e3849293b1) that has been replaced with a multi-select. We also have a few built-in genomes that we use with cuffmerge. When I choose the first GTF file (using locally cached sequence data) it will populate the reference genome correctly with our built-in genomes. However, once I choose more than one GTF file, I get one of two errors:

 No reference genome is available for the build associated with the selected input dataset
OR
 An invalid option was selected, please verify

The built-in genomes are definitely there and available for cuffmerge, but for some reason choosing more than one GTF file in the multi-select causes an error. Is this a bug or am I doing something wrong?

- Nik.



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)

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Re: problem with latest toolshed devteam cuffmerge wrapper multi-select

Nikhil Joshi-2
And, yes, all of the gtf files have the correct database build associated with them.

On Wed, Feb 18, 2015 at 6:29 PM, Nikhil Joshi <[hidden email]> wrote:
Hi all,

We run our own custom galaxy instance in the Amazon Cloud and I am updating our instance with the latest toolshed files. For cuffmerge, in past revisions, we would just have a button to add another GTF input. However, this latest one (10:b6e3849293b1) that has been replaced with a multi-select. We also have a few built-in genomes that we use with cuffmerge. When I choose the first GTF file (using locally cached sequence data) it will populate the reference genome correctly with our built-in genomes. However, once I choose more than one GTF file, I get one of two errors:

 No reference genome is available for the build associated with the selected input dataset
OR
 An invalid option was selected, please verify

The built-in genomes are definitely there and available for cuffmerge, but for some reason choosing more than one GTF file in the multi-select causes an error. Is this a bug or am I doing something wrong?

- Nik.



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)

___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

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  http://galaxyproject.org/search/mailinglists/
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Re: problem with latest toolshed devteam cuffmerge wrapper multi-select

Nikhil Joshi-2
So I am doing some debugging and it looks like in the from_html function in the SelectToolParameter class, it gets the legal values for the build using the get_legal_values function. This returns the correct values when I choose only one gtf file, but when I choose multiple gtf files the list of legal values is empty. I haven't figured out why this is happening.
- Nik.

On Wed, Feb 18, 2015 at 10:45 PM, Nikhil Joshi <[hidden email]> wrote:
And, yes, all of the gtf files have the correct database build associated with them.

On Wed, Feb 18, 2015 at 6:29 PM, Nikhil Joshi <[hidden email]> wrote:
Hi all,

We run our own custom galaxy instance in the Amazon Cloud and I am updating our instance with the latest toolshed files. For cuffmerge, in past revisions, we would just have a button to add another GTF input. However, this latest one (10:b6e3849293b1) that has been replaced with a multi-select. We also have a few built-in genomes that we use with cuffmerge. When I choose the first GTF file (using locally cached sequence data) it will populate the reference genome correctly with our built-in genomes. However, once I choose more than one GTF file, I get one of two errors:

 No reference genome is available for the build associated with the selected input dataset
OR
 An invalid option was selected, please verify

The built-in genomes are definitely there and available for cuffmerge, but for some reason choosing more than one GTF file in the multi-select causes an error. Is this a bug or am I doing something wrong?

- Nik.



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)

___________________________________________________________
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: problem with latest toolshed devteam cuffmerge wrapper multi-select

Nicola Soranzo-2
Hi Nikhil,
I would suggest to open an issue on https://github.com/galaxyproject/tools-devteam/issues

Best,
Nicola

Il 20.02.2015 10:28 Nikhil Joshi ha scritto:

So I am doing some debugging and it looks like in the from_html function in the SelectToolParameter class, it gets the legal values for the build using the get_legal_values function. This returns the correct values when I choose only one gtf file, but when I choose multiple gtf files the list of legal values is empty. I haven't figured out why this is happening.
- Nik.

On Wed, Feb 18, 2015 at 10:45 PM, Nikhil Joshi <[hidden email]> wrote:
And, yes, all of the gtf files have the correct database build associated with them.

On Wed, Feb 18, 2015 at 6:29 PM, Nikhil Joshi <[hidden email]> wrote:
Hi all,

We run our own custom galaxy instance in the Amazon Cloud and I am updating our instance with the latest toolshed files. For cuffmerge, in past revisions, we would just have a button to add another GTF input. However, this latest one (10:b6e3849293b1) that has been replaced with a multi-select. We also have a few built-in genomes that we use with cuffmerge. When I choose the first GTF file (using locally cached sequence data) it will populate the reference genome correctly with our built-in genomes. However, once I choose more than one GTF file, I get one of two errors:

 No reference genome is available for the build associated with the selected input dataset
OR
 An invalid option was selected, please verify
The built-in genomes are definitely there and available for cuffmerge, but for some reason choosing more than one GTF file in the multi-select causes an error. Is this a bug or am I doing something wrong?

- Nik.



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)



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Re: problem with latest toolshed devteam cuffmerge wrapper multi-select

John Chilton-4
In reply to this post by Nikhil Joshi-2
Is there any chance I can get you to reproduce this problem on the Galaxy test server: https://test.galaxyproject.org/root?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fcuffcompare%2Fcuffcompare%2F2.2.1.0 and then share the history with me ([hidden email])?

We have fixed some bugs related to this recently and it would be interesting to know if it works in the forthcoming release. My initial attempts to recreate with the latest release have failed so this might be fixed.

Any clue how old the Galaxy instance in your CloudMan setup is? I would be eager to try to fix problems in the 15.01 release as well - older than that though and we don't generally fix non-security related issues.

-John

On Fri, Feb 20, 2015 at 4:28 AM, Nikhil Joshi <[hidden email]> wrote:
So I am doing some debugging and it looks like in the from_html function in the SelectToolParameter class, it gets the legal values for the build using the get_legal_values function. This returns the correct values when I choose only one gtf file, but when I choose multiple gtf files the list of legal values is empty. I haven't figured out why this is happening.
- Nik.

On Wed, Feb 18, 2015 at 10:45 PM, Nikhil Joshi <[hidden email]> wrote:
And, yes, all of the gtf files have the correct database build associated with them.

On Wed, Feb 18, 2015 at 6:29 PM, Nikhil Joshi <[hidden email]> wrote:
Hi all,

We run our own custom galaxy instance in the Amazon Cloud and I am updating our instance with the latest toolshed files. For cuffmerge, in past revisions, we would just have a button to add another GTF input. However, this latest one (10:b6e3849293b1) that has been replaced with a multi-select. We also have a few built-in genomes that we use with cuffmerge. When I choose the first GTF file (using locally cached sequence data) it will populate the reference genome correctly with our built-in genomes. However, once I choose more than one GTF file, I get one of two errors:

 No reference genome is available for the build associated with the selected input dataset
OR
 An invalid option was selected, please verify

The built-in genomes are definitely there and available for cuffmerge, but for some reason choosing more than one GTF file in the multi-select causes an error. Is this a bug or am I doing something wrong?

- Nik.



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)



--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
<a href="tel:530.752.2698" value="+15307522698" target="_blank">530.752.2698 (w)

___________________________________________________________
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/


___________________________________________________________
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/