I agree with Nicola here! :)

Am 06.11.2014 um 17:48 schrieb Nicola Soranzo:
> Hi Pieter,
> you should probably add:
> 
> <action type="set_environment_for_install">
>   <repository name="prims_metabolomics_r_dependencies"
> owner="pieterlukasse">
>     <package name="R_bioc_metams" version="3.1.1" />
>   </repository>
> </action>
> 
> before using the R_ROOT_DIR environment variable.
> 
> Best,
> Nicola
> 
> Il 2014-11-06 11:28 Lukasse, Pieter ha scritto:
>> Hi Bjoern,
>>
>> I tried your suggestion, but it didn't work. So now I have split up
>> the R part from the Bioconductor part (blue and yellow below,
>> respectively). But the problem is that the <install> part executes
>> before the <package> part is finished and the $R_ROOT_DIR reference
>> also doesn't seem to work as I get the following error : " /bin/sh: 1:
>> /bin/Rscript: not found " . This R_ROOT_DIR is set by the <package>
>> script in my other tool_dependency.xml but is not visible in the
>> tool_dependency.xml below. But maybe I misunderstood what you meant by
>> "You can now access R_ROOT_DIR from any other tool_dependency file
>> ..."?
>>
>> <tool_dependency>
>>
>> <!-- see also http://wiki.galaxyproject.org/ToolShedToolFeatures for
>> syntax help
>>
>>  -->
>>
>>  <package name="R_bioc_metams" version="3.1.1">
>>
>>  <repository changeset_revision="0af753942e7b"
>> name="prims_metabolomics_dependencies" owner="pieterlukasse"
>> prior_installation_required="True"
>> toolshed="http://testtoolshed.g2.bx.psu.edu"; />
>>
>>  <install version="1.0">
>>
>>  <actions_group>
>>
>>  <!-- the Bioconductor and metaMS part -->
>>
>>  <action type="shell_command">wget -P $INSTALL_DIR
>>
>> http://testtoolshed.g2.bx.psu.edu/repos/pieterlukasse/prims_metabolomics/raw-file/tip/INSTALL.r</action>
>>
>>
>>
>>  <action type="shell_command">$R_ROOT_DIR/bin/Rscript
>> $INSTALL_DIR/INSTALL.r</action>
>>
>>  </actions_group>
>>
>>  </install>
>>
>>  </package>
>>
>>  <readme>
>>
>>  This dependency:
>>
>>  Ensures R 3.1.1 installation is triggered (via dependency).
>>
>>  Ensures Bioconductor 3.0 and package metaMS, multtest and snow are
>> installed.
>>
>>  </readme>
>>
>> </tool_dependency>
>>
>> Thanks,
>>
>> Pieter
>>
>> -----Original Message-----
>>  From: galaxy-dev-boun...@lists.bx.psu.edu
>> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Lukasse,
>> Pieter
>>  Sent: donderdag 6 november 2014 10:02
>>  To: 'Björn Grüning'; galaxy-dev@lists.bx.psu.edu; Dave Bouvier
>>  Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO
>> do this?
>>
>> Hi Bjoern,
>>
>> Thanks for this reply. I will have to try referring to the R_ROOT_DIR
>> from another tool_dependency. If it doesn't work I'll come back ;)
>>
>> Regards,
>>
>> Pieter
>>
>> -----Original Message-----
>>
>> From: Björn Grüning [mailto:bjoern.gruen...@gmail.com [1]]
>>
>> Sent: donderdag 30 oktober 2014 11:25
>>
>> To: galaxy-dev@lists.bx.psu.edu [2]; Lukasse, Pieter; Dave Bouvier
>>
>> Subject: Re: [galaxy-dev] Tool shed environment dependency - HOW TO do
>> this?
>>
>> Hi Pieter,
>>
>> Am 30.10.2014 um 11:15 schrieb Lukasse, Pieter:
>>
>>> Hi,
>>
>>>
>>
>>> I have a Bioconductor package which depends on R 3.1.1 , so I think
>> I cannot use the "setup_r_environment" trick.
>>
>> Why? Do you need a new release? The latest current release in the Tool
>> Shed is R 3.1.0. If this is not enough we need to poke Dave to build a
>> new package. But this way would be the preferred way.
>>
>>> I already got a tool_dependency.xml working that installs R 3.1.1
>> and the necessary Bioconductor packages using bioclite method (see
>> attachment). Now my question is:
>>
>>>
>>
>>>
>>
>>> * I would like to split up this into two steps as I don't want to
>> trigger the compilation of new R environment every time I when I need
>> to just update the
>>
>>> Bioconductor package....the question is: how to do such things in
>> general? How can I access the INSTALL_DIR of another tool from within
>> another tool_dependency.xml? If I can do this, then my problem is
>> solved.
>>
>> If you really want to build your R packages by your own. Have a look
>> at
>>
>> https://github.com/bgruening/galaxytools/blob/master/packages/package_r_3_0_3/tool_dependencies.xml
>>
>> [3]
>>
>> You will find an exhaustive installation instruction how to build R
>> properly. Also note that we export a variable called R_ROOT_DIR that
>> is set to $INSTALL_DIR. You can now access R_ROOT_DIR from any other
>> tool_dependency file ...
>>
>> Hope this helps,
>>
>> Bjoern
>>
>> P.S. Do you mind asking this question on biostar again, I think this
>> is a very nice question that can be of interest to a lot more people.
>>
>>> Thanks!
>>
>>>
>>
>>> Pieter Lukasse
>>
>>> Wageningen UR, Plant Research International Department of
>>
>>> Bioinformatics (Bioscience) Wageningen Campus, Building 107,
>>
>>> Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
>>
>>> T: +31-317481122;
>>
>>> M: +31-628189540;
>>
>>> skype: pieter.lukasse.wur
>>
>>> http://www.pri.wur.nl<http://www.pri.wur.nl/ [4]>
>>
>>>
>>
>>>
>>
>>>
>>
>>>
>>
>>> ___________________________________________________________
>>
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>>
>>>
>>
>>> To search Galaxy mailing lists use the unified search at:
>>
>>> http://galaxyproject.org/search/mailinglists/ [6]
>>
>>>
>>
>> ___________________________________________________________
>>
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>>
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>>
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>>
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>>
>> Links:
>> ------
>> [1] mailto:bjoern.gruen...@gmail.com
>> [2] mailto:galaxy-dev@lists.bx.psu.edu
>> [3]
>>
>> https://github.com/bgruening/galaxytools/blob/master/packages/package_r_3_0_3/tool_dependencies.xml
>>
>> [4] http://www.pri.wur.nl%3chttp:/www.pri.wur.nl/
>> [5] http://lists.bx.psu.edu/
>> [6] http://galaxyproject.org/search/mailinglists/
>> [7] http://lists.bx.psu.edu/
>> [8] http://galaxyproject.org/search/mailinglists/
> 
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