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 (jmchil...@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 <najo...@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 <najo...@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 <najo...@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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