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