Fwd: About Empty No Peek Problem

Question: Fwd: About Empty No Peek Problem

5.2 years ago by

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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modified 5.2 years ago by Björn Grüning • 350 • written 5.2 years ago by XiaoTao Jiang • 40

5.2 years ago by

Björn Grüning • 350

Björn Grüning • 350 wrote:

Hi Xiao, can you show us the complete wrapper XML script? Thanks, Bjoern

ADD COMMENT • link written 5.2 years ago by Björn Grüning • 350

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 REPLY • link written 5.2 years ago by XiaoTao Jiang • 40

Hi Xiao, the attached ones are working for me, hope for you too. Cheers, Bjoern

ADD REPLY • link written 5.2 years ago by Bjoern Gruening ♦ 5.1k

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 REPLY • link written 5.2 years ago by XiaoTao Jiang • 40

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 REPLY • link written 5.2 years ago by Bjoern Gruening ♦ 5.1k

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