problem with latest toolshed devteam cuffmerge wrapper multi-select
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 <https://toolshed.g2.bx.psu.edu/repository/view_changelog?id=84bbebf45888f374>) 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)
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 <najoshi@ucdavis.edu> 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 <https://toolshed.g2.bx.psu.edu/repository/view_changelog?id=84bbebf45888f374>) 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)
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 <najoshi@ucdavis.edu> 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 <najoshi@ucdavis.edu> 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 <https://toolshed.g2.bx.psu.edu/repository/view_changelog?id=84bbebf45888f374>) 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)
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
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: 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 wrote:
On Wed, Feb 18, 2015 at 6:29 PM, Nikhil
Joshi 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 [1]) 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
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
And, yes, all of the gtf files have the correct database build associated with them. 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: this a bug or am I doing something wrong?
- Nik.
--
Nikhil Joshi Bioinformatics Analyst/Programmer UC
Davis Bioinformatics Core
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
--
Nikhil Joshi
Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ [4] najoshi -at- ucdavis -dot- edu 530.752.2698 (w)
--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/ [6]
najoshi -at- ucdavis -dot- edu 530.752.2698 (w)
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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%2... and then share the history with me (jmchilton@gmail.com)? 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 <najoshi@ucdavis.edu> 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 <najoshi@ucdavis.edu> 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 <najoshi@ucdavis.edu> 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 <https://toolshed.g2.bx.psu.edu/repository/view_changelog?id=84bbebf45888f374>) 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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participants (3)
-
John Chilton -
Nicola Soranzo -
Nikhil Joshi