Hi Nicola

It happens with both versions available on the main toolshed. We originally had 
the package from bhaas, latest revision from 2012 and yesterday I installed the 
one from biomonika which requires package_trinityrnaseq_2013_08_14 (which in 
turn downloads a copy of trinity).
Both have the same problem.

Since a None value for the strand-spec. parameter means that the parameter is 
ignored (in the Cheetah code) I would think that the issue does not go down to 
the tool level (I can run Trinity on the command line just fine without 
specifying the strand-spec.)


On 08/05/15 17:51, Nicola Soranzo wrote:
Hi Christian,
was the trinityrnaseq tool installed from the Tool Shed? Which repository? Just 
to check this is not a tool problem.


Il 08.05.2015 10:44 Christian Schudoma (TSL) ha scritto:

Hi all,

I have encountered a problem when trying to run trinityrnaseq (Galaxy Tool 
Version 0.0.1) from Galaxy. Leaving the strand-specificity input parameter as 
"None" will prevent the form from being submitted. Instead, the 
strand-specificity input box will be highlighted in red and I'm asked to 
"Please verify this parameter."

Before the last update we were running a very very old instance of Galaxy (I 
think the update before the last was in 2013) from which we could submit 
trinity-jobs just fine. I found a commit from Aysam from late 2014 which does 
something in the immediate vicinity of the "Please verify this parameter" - 
message. (https://bitbucket.org/galaxy/galaxy-central/commits/bda732e549b7/), 
which I am guessing could have something to do with it.

Anyone got any ideas regarding this? Any help would be appreciated.


Dr. Christian Schudoma
Bioinformatics Support Officer

Bioinformatics Group
The Sainsbury Laboratory
Norwich Research Park
Norwich NR4 7UH
United Kingdom
+44 (0) 1603 450 601
twitter: @cpt_bwt

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