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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[3]
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