The problem is not in the Cheetah code, which does not get executed because of the validation error.
I think this a Galaxy bug which tries to validate the parameter values but interprets the value "None" of the library_type param as "no option selected".
Nicola
Il 08.05.2015 19:18 Christian Schudoma (TSL) ha scritto:
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.)
Thanks
Christian
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.
Cheers,
Nicola
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/ [1]), which I am guessing could have something to do with it.
Anyone
got any ideas regarding this? Any help would be appreciated.
Thanks
Christian
-- Dr. Christian Schudoma
Bioinformatics Support Officer
Bioinformatics Group The
Sainsbury Laboratory
Norwich Research Park Norwich NR4 7UH
United Kingdom
+44 (0) 1603 450
601
christian.schudoma@tsl.ac.uk [2] twitter: @cpt_bwt
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