Hi Xiao,

can you show us the complete wrapper XML script?

Thanks,
Bjoern

>
>
> ---------- Forwarded message ----------
> From: XiaoTao Jiang <biofuture.jiang@gmail.com>
> Date: 2013/9/2
> Subject: About empty no peek problem
> To: galaxy-user-request@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
>
>
>
>

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