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