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
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