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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