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 > > > >

> ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/

Hi,

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

Great!

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?

It has nothing to do with the interpreter. Its recommended to use the "${}" notation. You never know if your path to input or output has some white spaces or other pitfalls included. Ciao! Bjoern

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 > > > > > > > > > > > ___________________________________________________________ > > The Galaxy User list should be used for the discussion of > > Galaxy analysis and other features on the public server > > at usegalaxy.org. Please keep all replies on the list by > > using "reply all" in your mail client. For discussion of > > local Galaxy instances and the Galaxy source code, please > > use the Galaxy Development list: > > > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > > > To manage your subscriptions to this and other Galaxy lists, > > please use the interface at: > > > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > > > http://galaxyproject.org/search/mailinglists/ > > > > >