Fwd: About empty no peek problem

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Fwd: About empty no peek problem

XiaoTao Jiang


---------- Forwarded message ----------
From: XiaoTao Jiang <[hidden email]>
Date: 2013/9/2
Subject: About empty no peek problem
To: [hidden email]


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/

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Re: Fwd: About empty no peek problem

Björn Grüning
Hi Xiao,

can you show us the complete wrapper XML script?

Thanks,
Bjoern

>
>
> ---------- Forwarded message ----------
> From: XiaoTao Jiang <[hidden email]>
> Date: 2013/9/2
> Subject: About empty no peek problem
> To: [hidden email]
>
>
> 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/



___________________________________________________________
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/
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Re: Fwd: About empty no peek problem

XiaoTao Jiang
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 <[hidden email]>
Hi Xiao,

can you show us the complete wrapper XML script?

Thanks,
Bjoern

>
>
> ---------- Forwarded message ----------
> From: XiaoTao Jiang <[hidden email]>
> Date: 2013/9/2
> Subject: About empty no peek problem
> To: [hidden email]
>
>
> 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/





___________________________________________________________
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/

bar_plot.xml (606 bytes) Download Attachment
barchart.r (1K) Download Attachment
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Re: Fwd: About empty no peek problem

Björn Grüning-2
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 <[hidden email]>
>         Hi Xiao,
>        
>         can you show us the complete wrapper XML script?
>        
>         Thanks,
>         Bjoern
>        
>         >
>         >
>         > ---------- Forwarded message ----------
>         > From: XiaoTao Jiang <[hidden email]>
>         > Date: 2013/9/2
>         > Subject: About empty no peek problem
>         > To: [hidden email]
>         >
>         >
>         > 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/
>        
>        
>        
>
>


___________________________________________________________
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/

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Re: Fwd: About empty no peek problem

XiaoTao Jiang
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 <[hidden email]>
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 <[hidden email]>
>         Hi Xiao,
>
>         can you show us the complete wrapper XML script?
>
>         Thanks,
>         Bjoern
>
>         >
>         >
>         > ---------- Forwarded message ----------
>         > From: XiaoTao Jiang <[hidden email]>
>         > Date: 2013/9/2
>         > Subject: About empty no peek problem
>         > To: [hidden email]
>         >
>         >
>         > 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/
>
>
>
>
>




___________________________________________________________
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/
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Re: Fwd: About empty no peek problem

Björn Grüning-2
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 <[hidden email]>
>         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
>         <[hidden email]>
>         >         Hi Xiao,
>         >
>         >         can you show us the complete wrapper XML script?
>         >
>         >         Thanks,
>         >         Bjoern
>         >
>         >         >
>         >         >
>         >         > ---------- Forwarded message ----------
>         >         > From: XiaoTao Jiang <[hidden email]>
>         >         > Date: 2013/9/2
>         >         > Subject: About empty no peek problem
>         >         > To: [hidden email]
>         >         >
>         >         >
>         >         > 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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>        
>        
>
>



___________________________________________________________
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