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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