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/
    >
    >
    >
    >
    >