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.schud...@tsl.ac.uk [2] >>> twitter: @cpt_bwt >> >> Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. >> E chiami gratis anche i numeri fissi e mobili nel mondo! >> Scarica subito l'app Vai su https://www.indoona.com/ [3] Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/
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