Hi Björn, I'm a bit old fashioned and think I prefer a proper Galaxy tool rather than a notebook :) so I've set up a temporary demonstration/test site of a toolfactory generated tool that does what I think I need - can some kind soul please test it and let me know how it goes ? If it's useful, it needs to be adjusted to depend on whatever version of package_R you want to work with - currently just uses the system R for demonstration purposes.
I used the toolfactory2 (main toolshed) (which now allows any number of (optionally non editable) parameters!!!) to wrap the script shown at the bottom of https://wiki.galaxyproject.org/SetUpREnvironment. There are currently three parameters - the names of the R/BioC packages from sessionInfo(), the local directory where all the tarballs should be stowed and the XML output prefix to prepend to each row of the generated XML stanza for tool_dependencies.xml The resulting toolshed tarball was uploaded to a local toolshed and then installed to produce a new tool in the "tool generators" section - r_bioc_depgen Generate dependencies for R/BioC packages If you import the history at http://130.56.252.21/history/list_published you will see the toolfactory job (#1,#2,#3) - rerunning will show how the parameters are defined - fugly but it does work. After generating/uploading/installing the new tool, outputs from a test run are in #4 and #5 for DESeq Comments and suggestions welcomed! On Sun, Jan 11, 2015 at 10:41 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote: > Hi Ross, > > you are absolutely right. > My download_store repository is exactly for this purpose. > > https://github.com/bgruening/download_store > > If you are interested we could integrate your additional magic into the > notebook. > > Thanks, > Bjoern > > Am 11.01.2015 um 01:33 schrieb Ross: > > Hi, Björn, > > Looks pretty similar! > > Aren't the links your notebook generates transient? I think if you put > them > > into a tool_dependencies.xml, they will fail permanently immediately > after > > any of the package authors updates one of the relevant svn repositories? > > > > AFAIK, it looks like the whole BioC/CRAN infrastructure is automated so a > > link that works today like > > http://cran.fhcrc.org/src/contrib/Rcpp_0.11.3.tar.gz will fail when Rcpp > > next gets updated and Rcpp_0.11.3.tar.gz is migrated to > > http://cran.fhcrc.org/src/contrib/00Archive/Rcpp/ with a replacement > (eg) > > http://cran.fhcrc.org/src/contrib/Rcpp_0.11.4.tar.gz appearing in the > > contrib directory? > > > > That's why my more complex script downloads all the latest archives into > my > > local github archive repo and generates a permanent link to suit that > > github repo. > > We definitely need an automated solution as this is a really infuriating > > aspect of trying to make code relying on R/BioC packages reproducible. > > > > > > On Thu, Jan 8, 2015 at 11:28 PM, Björn Grüning < > bjoern.gruen...@gmail.com> > > wrote: > > > >> Hi Ross, > >> > >> this is great! > >> Have you seen this notebook? > >> > >> > >> > http://nbviewer.ipython.org/github/bgruening/notebooks/blob/master/R/extract_all_dependencies_from_an_r_package.ipynb > >> > >> It tries to do the same thing. Maybe it's also worth to mention? Maybe > >> we can enhance it? > >> > >> Thanks, > >> Bjoern > >> > >> Am 08.01.2015 um 08:09 schrieb Ross: > >>> This may be helpful for anyone else struggling to get complex nested R > >>> package dependency installation from the tool shed sorted out. That > whole > >>> can of worms. While we have setup_r_packages, the developer still has > to > >>> figure out the right magical incantation and make sure the tarballs are > >>> available. > >>> > >>> https://wiki.galaxyproject.org/SetUpREnvironment has some notes I've > >>> started - contribitions welcome. > >>> > >>> It has a more or less reusable R script to generate > tool_dependencies.xml > >>> boilerplate, assuming you set the constant libdir to your local git > >>> repository path where those tarballs will be downloaded from. > >>> > >>> I hope this helps someone! > >>> > >>> Could make a tool to do this if enough developers want access to it > >> without > >>> the pain of managing yet another R script? > >>> > >> > > >
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