Hi Nicola
It happens with both versions available on the main toolshed. We originally had the
Both have the same
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: 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). 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.)
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
Before the last update we were running a very very
Thanks 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." 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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