Thanks for this. I just opened the 3.2.1-goolf-1.7.20 easyconfig PR. I'll see if we should update any extensions.
Did you see the new Bioconductor Bundle (to separate it from the core?) On Wed, Jul 22, 2015 at 10:43 AM Pieter Neerincx <[email protected]> wrote: > Hi all, > > It took a little longer, but I think I now have a fully functional > generateEasyConfig.R script that is ready for distribution; "It works on > our clusters" :)... I've requested access to > > https://github.com/fgeorgatos/easybuild.experimental > > by creating an "issue" as per instructions in the README.md, but it looks > like Fotis Georgatos is on holiday... For now I forked the repo and > published the generator here: > > > https://github.com/pneerincx/easybuild.experimental/blob/master/users/pneerincx/generateEasyConfig.R > > DISCLAIMER 1: The generated easyconfig will contain any packages you had > installed and which are available from CRAN or BioConductor repo's. > If you have R packages from elsewhere you may have to tweak > the generator. > > DISCLAIMER 2: The generator assumes you will want an R with graphics > capabilities for plotting. Therefore it includes dependencies on > easyconfigs for various libs. > For libpng-1.6.17 and freetype-2.6 I had to create new > easyconfigs and patches as these libs contain bugs and some R packages fail > to compile with the plain vanilla libs. > I'll create a pull request for these new easyconfigs, but it > will take some time before these are available from the latest and greatest > EasyBuild release... > > Cheers, > > Pi > > > On Jun 29, 2015, at 6:00 PM, Pablo Escobar Lopez < > [email protected]> wrote: > > > ok, thanks for your effort Pieter > > > > 2015-06-29 16:25 GMT+02:00 Pieter Neerincx <[email protected]>: > > > > On Jun 29, 2015, at 3:37 PM, Pablo Escobar Lopez < > [email protected]> wrote: > > > > > > > > > > > 2015-06-24 10:58 GMT+02:00 Pieter Neerincx <[email protected] > >: > > > > > > Yesterday I started working on an R-script that generates an *.eb from > an existing R installation. This is based on Stefano's code (Many thanks > for sharing that!) and adds some commandline switches, help and code to > figure out whether a package came from a CRAN repo or from BioConductor. > Hence this is slightly different compared to the above as it generates a > complete *.eb from pure R, but I can easily add an option to only generate > a pkglist file, which may then be used by an existing *.eb. > > > > > > Is it Ok if I add this with a README to the ..../r/R/ dir in the > EasyConfigs repo and create a pull request or would you prefer this kind of > supplementary code to go elsewhere? > > > > > > > > > > > > is this code published somewhere? > > > > As soon as I solved the last bugs I'll publish and report back to this > list... > > > > Cheers, > > > > Pi > > > > > thanks > > > Pablo. > > > > > > > > > > > > -- > > > Pablo Escobar López > > > HPC systems engineer > > > Biozentrum, University of Basel > > > Swiss Institute of Bioinformatics SIB > > > Email: [email protected] > > > Phone: +41 61 267 21 80 > > > http://www.biozentrum.unibas.ch > > > > ------------------------------------------------------------- > > phone: +31 6 143 66 783 > > e-mail: [email protected] > > skype: pieter.online > > ------------------------------------------------------------- > > > > > > > > > > -- > > Pablo Escobar López > > HPC systems engineer > > Biozentrum, University of Basel > > Swiss Institute of Bioinformatics SIB > > Email: [email protected] > > Phone: +41 61 267 21 80 > > http://www.biozentrum.unibas.ch > > ------------------------------------------------------------- > phone: +31 6 143 66 783 > e-mail: [email protected] > skype: pieter.online > ------------------------------------------------------------- > >
