> Date: Tue, 12 Aug 2014 08:58:38 -0400
> From: jmchilton@gmail.com
> To: nate@bx.psu.edu
> CC: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] TypeError with 'dict'
>
> Nate is right - full traceback would help. I am not sure it is the
> only problem - but these outputs do not look right:
>
> <outputs>
> <data format="tabular" name="Project" label="Project"
> from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input"/>
> <data format="tabular" name="Samples" label="Samples"
> from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples"/>
> </outputs>
>
> Galaxy isn't going to expand variables ($Project.input /
> $Project.samples) in the from_work_dir attribute so those are going to
> be taken as literal strings. That directory also really needs to be
> relative to the tool directory and I believe this is enforced for
> security reasons.
>
> -John
>
>
> On Tue, Aug 12, 2014 at 8:55 AM, Nate Coraor <nate@bx.psu.edu> wrote:
> > Hi Martin,
> >
> > If there's a full traceback instead of just this fragment, that'd certainly
> > help with determining exactly where the problem is coming from.
> >
> > --nate
> >
> > On Aug 12, 2014, at 4:17 AM, bjoern.gruening@googlemail.com
> > <bjoern.gruening@gmail.com> wrote:
> >
> > Hi,
> >
> > Galaxy stores all information about a tool and it's parameters in a
> > database.
> > I suppose if something is wrong with your tool, under some circumstances, it
> > can't be stored in the database.
> >
> > Cheers,
> > Bjoern
> >
> >
> > 2014-08-12 9:23 GMT+02:00 Martin Christiansen
> > <martinchristiansendk@hotmail.com>:
> >>
> >> Hi Björn,
> >>
> >> I'm using galaxy as a front-end to run a larger pipeline in the
> >> background.
> >> Originally I implemented the pipeline which had the same wrapper and was
> >> running fine.
> >> I have now begun to break it down into steps where this is the first step.
> >>
> >> The only thing I've changed is the output.
> >> How would this cause an error in the python egg?
> >>
> >> Martin
> >>
> >> > Date: Tue, 12 Aug 2014 09:06:51 +0200
> >> > From: bjoern.gruening@gmail.com
> >> > To: martinchristiansendk@hotmail.com; galaxy-dev@lists.bx.psu.edu
> >> > Subject: Re: [galaxy-dev] TypeError with 'dict'
> >>
> >> >
> >> > Hi Martin,
> >> >
> >> > please keep galaxy-dev in the CC list.
> >> >
> >> > Am 12.08.2014 um 08:51 schrieb Martin Christiansen:
> >> > > Hi Björn,
> >> > >
> >> > > Most certainly. I have posted it below.
> >> > >
> >> > > <tool id="screen_reads" name="Screen Reads">
> >> >
> >> > -> add here a version number version="0.1"
> >> >
> >> > > <description>against hg19</description>
> >> > >
> >> > > <command interpreter="bash">screen_reads.sh $Project.input
> >> > > $Project.samples $Project $Samples </command>
> >> > >
> >> > > <inputs>
> >> > > <conditional name="Project">
> >> > > <param name="input" type="select" label="Select project">
> >> > > <option value="galaxy_test1">galaxy_test1</option>
> >> > > <option value="Untitled Folder">Untitled Folder</option>
> >> >
> >> > -> is the white space really needed? If so $Project.input will be two
> >> > words. Use "${Project.input}" to convert it to onw argument
> >> >
> >> > > </param>
> >> > > <when value="galaxy_test1">
> >> > > <param name="samples" type="select" label="Select samples"
> >> > > display="checkboxes" multiple="True">
> >> > > <option value="147406386-700171390">147406386-700171390</option>
> >> > > <option value="158256496-700097688">158256496-700097688</option>
> >> > > <option value="158337416-700013715">158337416-700013715</option>
> >> > > <option value="158337416-700097837">158337416-700097837</option>
> >> > > <option value="158357646-700035237">158357646-700035237</option>
> >> > > <option value="158458797-700014562">158458797-700014562</option>
> >> > > <option value="158479027-700014724">158479027-700014724</option>
> >> > > <option value="158479027-700097196">158479027-700097196</option>
> >> > > <option value="158499257-700014837">158499257-700014837</option>
> >> > > <option value="158499257-700098561">158499257-700098561</option>
> >> > > <option value="158742018-700015181">158742018-700015181</option>
> >> > > <option value="158802708-700015245">158802708-700015245</option>
> >> > > <option value="158802708-700015250">158802708-700015250</option>
> >> > > <option value="158802708-700099803">158802708-700099803</option>
> >> > > <option value="158802708-700119165">158802708-700119165</option>
> >> > > <option value="158822939-700014954">158822939-700014954</option>
> >> > > <option value="158883629-700015113">158883629-700015113</option>
> >> > > <option value="158883629-700100227">158883629-700100227</option>
> >> > > <option value="158883629-700112812">158883629-700112812</option>
> >> > > <option value="158924089-700099307">158924089-700099307</option>
> >> > > </param>
> >> > > </when>
> >> > > <when value="Untitled Folder">
> >> > > <param name="samples" type="select" label="Select samples"
> >> > > display="checkboxes" multiple="True">
> >> >
> >> > -> you don't have any <option> here.
> >> >
> >> > > </param>
> >> > > </when>
> >> > > </conditional>
> >> > > </inputs>
> >> > >
> >> > > <outputs>
> >> > > <data format="tabular" name="Project" label="Project"
> >> > > from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.input"/>
> >> > > <data format="tabular" name="Samples" label="Samples"
> >> > > from_work_dir="/eva/projects/smash/MOCAT/test/martin/$Project.input/$Project.samples"/>
> >> > > </outputs>
> >> >
> >> > -> I'm not sure this will work. workdir is a special dir Galaxy creates
> >> > for you. It will be the working directory where your program get's
> >> > called. So assume your program creates foo.sam files. You can specify it
> >> > like from_work_dir='foo.sam'
> >> >
> >> > The input handling looks also a little bit strange. You do not specify
> >> > any input file in Galaxy. That is not really Galaxy like :)
> >> >
> >> > Cheers,
> >> > Bjoern
> >> >
> >> > > <help>
> >> > > Reads screened against hg19.
> >> > > </help>
> >> > > </tool>
> >> > >
> >> > > Best,
> >> > > Martin
> >> > >
> >> > >
> >
> >
> > ___________________________________________________________
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> >
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