Hi Bjorn, Thanks for caring :) R/Bioc dependencies are determined by the target R package. This realisation made me change tool factory 2 in the test toolshed so it now allows R (or perl or python - not bash!) dependency package_r_ selection. It still allows the local system R but that's not recommended for anything reproducible. The generated tool will always use that R and so I can generate an RBioC dependency generator using that script https://wiki.galaxyproject.org/SetUpREnvironment for any available toolshed package_r_ Feedback always appreciated...
On Sun, Jan 18, 2015 at 9:25 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote: > Hi Ross, > > Am 13.01.2015 um 00:13 schrieb Ross: > > 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 > > This is cool! > I have to try this on a few packages! > This could also be of interest for our GSOC idea: > > https://wiki.galaxyproject.org/Develop/GSOC/2015Ideas#Fostering_Bioconductor_Collaborations > > Thanks Ross for working on this! > Bjoern > > > 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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