Hi Stef,

fortunately it is way easier than that. Please have a look at the "setup_r_environment" installation routine :)


Cheers,
Bjoern

Am 17.06.2014 11:07, schrieb Stef van Lieshout:
Say option 3 is the way to go, would you say every new version of an R
package should be wrapped in a new galaxy package (and give them names
like "matrixStats_0_10_0") or create one package ("matrixStats") and
update that one if a new version is worth an update. In the first way
there would be an enormous amount of packages ;)

Also if you do need an external R script as you say, how would I
construct my tool_dependencies.xml to execute R code?

And last, if that approach doesn't work out for me, how can copy a file
in the repository to the installation dir? (to execute it with Rscript)

Many thanks,
Stef


----- Original message -----
From: "Kandalaft, Iyad" <iyad.kandal...@agr.gc.ca>
To: Stef van Lieshout <stefvanliesh...@fastmail.fm>,
"galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: RE: [galaxy-dev] R bioconductor dependencies when creating
toolshed installation
Date: Mon, 16 Jun 2014 18:19:46 +0000

I would typically recommend Option 3 as it is the best practice.
However, human resources limit this as a viable option even though this
should be the "Gold Standard" that you aim for.  This allows you to
reuse the dependencies later for other tool wrappers AND you don't have
to re-install dependencies every time you make a modification to your
tool wrapper repository.  While briefly looking at Bioconductor, it
seems that they keep old version of packages (ex:
http://www.bioconductor.org/packages/2.13/data/experiment/bin/windows/contrib/3.0/AmpAffyExample_1.2.13.zip),
where using the URLs directly might be advantageous if their BiocLite
doesn't allow you to define which version to install.  You don't
necessarily need to have an external R script for the installation
because many of these commands can be done within the
tool_dependencies.xml.

Regards,


Iyad Kandalaft
Microbial Biodiversity Bioinformatics
Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire Canada
960 Carling Ave.| 960 Ave. Carling
Ottawa, ON| Ottawa (ON) K1A 0C6
E-mail Address / Adresse courriel  iyad.kandal...@agr.gc.ca
Telephone | Téléphone 613-759-1228
Facsimile | Télécopieur 613-759-1701
Teletypewriter | Téléimprimeur 613-773-2600
Government of Canada | Gouvernement du Canada



-----Original Message-----
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Stef van
Lieshout
Sent: Monday, June 16, 2014 10:04 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] R bioconductor dependencies when creating toolshed
installation

Hi all,

I'm running into some difficulties on how to setup the installation
procedure for a galaxy tool which executes an R script and has certain
dependencies (mainly bioconductor packages). R can deal with
dependencies, packages can be installed with install.packages (has a
"dependencies" argument) or biocLite() for bioconductor packages.

Yet, now I want my tool to be available at toolsheds. To do this I see
several options:

1) setting up tool_dependencies.xml with "R CMD INSTALL" for all
packages. BUT: need to download all dependencies before install, and can
older versions still be downloaded? Maybe need to upload them to
toolshed too..

2) setting up tool_dependencies.xml to call an installation script with
Rscript (where I could use install.packages), BUT: Dependencies are
taken care of. But how do I select specific (older) versions, because if
I dont, installing at different time can give different version.

3) creating a repository for each package and have all of them as
requirement in my galaxy tool. BUT: a lot of work for a lot of
dependencies

All have pros and cons, how do people deal with this?

Stef
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  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/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  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/

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  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/

Reply via email to