Question: Fwd: About Empty No Peek Problem
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gravatar for XiaoTao Jiang
5.0 years ago by
XiaoTao Jiang40 wrote:
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
galaxy • 1.6k views
ADD COMMENTlink modified 5.0 years ago by Björn Grüning350 • written 5.0 years ago by XiaoTao Jiang40
0
gravatar for Björn Grüning
5.0 years ago by
Björn Grüning350 wrote:
Hi Xiao, can you show us the complete wrapper XML script? Thanks, Bjoern
ADD COMMENTlink written 5.0 years ago by Björn Grüning350
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>
ADD REPLYlink written 5.0 years ago by XiaoTao Jiang40
Hi Xiao, the attached ones are working for me, hope for you too. Cheers, Bjoern
ADD REPLYlink written 5.0 years ago by Bjoern Gruening5.1k
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 "${output}". What is the inner reason for it? Cheers! Xiaotao 2013/9/3 Bjoern Gruening <bjoern.gruening@gmail.com>
ADD REPLYlink written 5.0 years ago by XiaoTao Jiang40
Hi, Great! It has nothing to do with the interpreter. Its recommended to use the "${}" notation. You never know if your path to input or output has some white spaces or other pitfalls included. Ciao! Bjoern
ADD REPLYlink written 5.0 years ago by Bjoern Gruening5.1k
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