This tool is only useful for developers - but it serves as an example of what the TF2 can do relatively quickly. Using the TF2, the script was processed to create a new special purpose tool. However, the illustration is complicated by the task - so first you might need to read about why the script was needed in the first place, then about how it was re-cast as a Tool Factory (TF2) script by adding biolerplate code (copied from the TF2 tool examples) to read parameters. This page currently documents converting what started out as a hacky R script (see end) to generate all package dependencies for a new tool I was wrapping, into a reusable hacky tool any developer can use, available from the test toolshed under tool generators as "biocdepgen" for installation into any non-critical (please, not production) Galaxy dev instance - see \_3\_1\_2 Using the Tool Factory to make writing R/BioC tools easier R/BioC devs might like to try Rgalaxy which runs inside R and does some of the templating by introspecting the R code. Although the impermanence of the URLs that notebook generates at the moment may be a problem. For alternative approaches to this challenge, see Bjöaut rn Grüaut ning's iPython notebook.
Executive Summaryĭescribes using the Galaxy Tool Factory 2 to make a new tool to automate one very tedious and gnarly part of writing shareable, repeatable, self installing Galaxy analysis tools that use specific versions of R, R/BioConductor packages and their entire dependency chain. This document assumes technical familiarity with R/BioConductor and a good understanding of how the Galaxy Tool Shed automates tool installation.
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