Dear Bjorn

The configure xml file and the relevant R scripts is attached.

Thank you for all your help.

Regards,
XiaoTao
The University of HongKong


2013/9/3 Björn Grüning <bjoern.gruen...@pharmazie.uni-freiburg.de>

> Hi Xiao,
>
> can you show us the complete wrapper XML script?
>
> Thanks,
> Bjoern
>
> >
> >
> > ---------- Forwarded message ----------
> > From: XiaoTao Jiang <biofuture.ji...@gmail.com>
> > Date: 2013/9/2
> > Subject: About empty no peek problem
> > To: galaxy-user-requ...@lists.bx.psu.edu
> >
> >
> > Dear all
> >
> >
> > Today I embed one of my R script into local galaxy, I have encountered
> > a strange problem.  The script can successfully in local. However,
> > when I run it online in galaxy, the output file is empty and in
> > history panel, it display empty and no peek.
> >
> >
> > I searched the mailing list, but still can not find solutions to solve
> > it.
> >
> >
> > The command display in sever is : key part
> >
> >
> > galaxy.jobs.runners.local DEBUG 2013-09-02 17:29:49,297 executing: R
> > CMD BATCH --slave
> > "--args
> /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat
> /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat"
> barchart.r
> > galaxy.jobs.runners.local DEBUG 2013-09-02 17:29:49,493 execution
> > finished: R CMD BATCH --slave
> > "--args
> /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat
> /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat"
> barchart.r
> > galaxy.jobs DEBUG 2013-09-02 17:29:49,538 Tool did not define exit
> > code or stdio handling; checking stderr for success
> > galaxy.tools DEBUG 2013-09-02 17:29:49,697 Error opening galaxy.json
> > file: [Errno 2] No such file or directory:
> >
> '/Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/job_working_directory/000/71/galaxy.json'
> > galaxy.jobs DEBUG 2013-09-02 17:29:49,759 job 71 ended
> >
> >
> > I check the generated output file
> >
>  
> /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat
> >
> >
> > It is empty zero in size
> >
> >
> > and then I run the command in local command
> >
> >
> > R CMD BATCH --slave
> > "--args
> /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_44.dat
> /Users/jiangxiaotao/Programe/galaxy-galaxy-dist-a4113cc1cb5e/database/files/000/dataset_64.dat"
> barchart.r
> >
> >
> >
> > The output is correct.
> >
> >
> >
> >
> > Any suggestions will be appreciated !!
> >
> >
> > Xiaotao JIANG
> > Regards,
> > The University of HongKong
> > Department of Civil Engineering
> >
> >
> >
> >
> > ___________________________________________________________
> > The Galaxy User list should be used for the discussion of
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> >
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> >
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> >
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>
>
>
>
<tool id="hist_plot" name="Plot Histgrame for ARGs" version="1.0">
        <description>Bar Plot of Frequencies of ARGs</description>
        <command>R CMD BATCH --slave "--args $input $outpdf" barchart.r </command>
        <inputs>
                <param format="txt" name="input"  type="data" label="ARGs Frequence info" />
        </inputs>
        <outputs>
                <data format="pdf" name="outpdf" />
        </outputs>
</tool>

Attachment: barchart.r
Description: Binary data

___________________________________________________________
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use the Galaxy Development list:

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