Dear Bjoern

It 's OK now! Thank you for all your time on it.

When using R as the interpreter, why do we need to change the $input and $output into "${input}" and "${output}". What is the inner reason for it?

Cheers!
Xiaotao


2013/9/3 Bjoern Gruening <bjoern.gruening@gmail.com>
Hi Xiao,

the attached ones are working for me, hope for you too.

Cheers,
Bjoern

> 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.gruening@pharmazie.uni-freiburg.de>
>         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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