Difference between revisions of "R Portal"
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The R portal is not a production service yet. We're currently looking for R users who want to help us to make it work smoothly in a real-world setting. If you're interested, please [mailto:wvengen+lgi@nikhef.nl drop me a mail]. | The R portal is not a production service yet. We're currently looking for R users who want to help us to make it work smoothly in a real-world setting. If you're interested, please [mailto:wvengen+lgi@nikhef.nl drop me a mail]. | ||
| − | * [https:// | + | '''Note''' at this moment the LGI service is temporarily down because of hardware issues. We're sorry for the inconvenience and are working to get it back. |
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| + | * [https://koepoort.biggrid.nl/LGIportal/ Visit the R portal] ''(contact [mailto:wvengen+lgi@nikhef.nl wvengen+lgi@nikhef.nl] for an account)'' | ||
* read more about the [[LGI/Rlgi|Rlgi module]] for R. | * read more about the [[LGI/Rlgi|Rlgi module]] for R. | ||
* [http://www.nikhef.nl/~wvengen/pubs/20120217-bioassist_meeting.pdf Slides] of the R portal presentation at the [https://wiki.nbic.nl/index.php/BioAssist BioAssist] [https://wiki.nbic.nl/index.php/Agenda_BioAssist_Programmers_Meeting_2012/2/17 meeting] of Feb, 2012. | * [http://www.nikhef.nl/~wvengen/pubs/20120217-bioassist_meeting.pdf Slides] of the R portal presentation at the [https://wiki.nbic.nl/index.php/BioAssist BioAssist] [https://wiki.nbic.nl/index.php/Agenda_BioAssist_Programmers_Meeting_2012/2/17 meeting] of Feb, 2012. | ||
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Packages installed on the grid: <tt>affy affydata affyio affyPLM affyQCReport annaffy annotate base biomaRt bitops boot class cluster codetools datasets foreign gcrma genefilter geneplotter graphics grDevices grid hgu95av2.db IRanges KEGG.db KernSmooth lattice limma marray MASS Matrix methods mgcv multtest nlme nnet org.Hs.eg.db preprocessCore RColorBrewer RCurl Rlgi rpart RSQLite simpleaffy spatial splines stats stats4 survival tcltk tools utils vsn XML xtable</tt><br/> | Packages installed on the grid: <tt>affy affydata affyio affyPLM affyQCReport annaffy annotate base biomaRt bitops boot class cluster codetools datasets foreign gcrma genefilter geneplotter graphics grDevices grid hgu95av2.db IRanges KEGG.db KernSmooth lattice limma marray MASS Matrix methods mgcv multtest nlme nnet org.Hs.eg.db preprocessCore RColorBrewer RCurl Rlgi rpart RSQLite simpleaffy spatial splines stats stats4 survival tcltk tools utils vsn XML xtable</tt><br/> | ||
| − | Packages on the GPU cluster: <tt>base bitops boot class cluster codetools datasets foreign graphics grDevices grid KernSmooth lattice MASS Matrix methods mgcv nlme nnet Rcpp rgpu rgputools rpart snow spatial splines stats stats4 survival tcltk tools utils XML</tt><br/> | + | Packages on the GPU cluster: <tt>base bitops boot class cluster codetools datasets foreign graphics grDevices grid KernSmooth lattice MASS Matrix methods mgcv nlme nnet Rcpp rgpu rgputools rpart snow spatial splines stats stats4 survival tcltk tools utils XML</tt> <i>(pending: <tt>RCurl Rlgi</tt>)<br/> |
(you can still use <tt>[http://cran.r-project.org/doc/manuals/R-admin.html#installing-packages install.packages()]</tt> to install extra packages right now) | (you can still use <tt>[http://cran.r-project.org/doc/manuals/R-admin.html#installing-packages install.packages()]</tt> to install extra packages right now) | ||
Latest revision as of 13:15, 19 July 2012
The BiG Grid R portal
To make using the grid easier, we're working a portal for users of the statistical programming language R. It's a web interface for your jobs, and a module for R. Plus some tools and language bindings to interact with the jobs.
As a bonus, you can also use it to run R on a GPU cluster.
The R portal is not a production service yet. We're currently looking for R users who want to help us to make it work smoothly in a real-world setting. If you're interested, please drop me a mail.
Note at this moment the LGI service is temporarily down because of hardware issues. We're sorry for the inconvenience and are working to get it back.
- Visit the R portal (contact wvengen+lgi@nikhef.nl for an account)
- read more about the Rlgi module for R.
- Slides of the R portal presentation at the BioAssist meeting of Feb, 2012.
What's inside
The system is based on the Leiden Grid Intrastructure (LGI). It interacts with the grid using pilotjobs (read more).
- Leiden Grid Infrastructure(original source), including a number of tools
- lgipilot pilotjob manager
- LGIportal web portal
On the grid, R 2.11 and 2.12 are available; the gpu cluster has versions 2.12 and 2.13.
Packages installed on the grid: affy affydata affyio affyPLM affyQCReport annaffy annotate base biomaRt bitops boot class cluster codetools datasets foreign gcrma genefilter geneplotter graphics grDevices grid hgu95av2.db IRanges KEGG.db KernSmooth lattice limma marray MASS Matrix methods mgcv multtest nlme nnet org.Hs.eg.db preprocessCore RColorBrewer RCurl Rlgi rpart RSQLite simpleaffy spatial splines stats stats4 survival tcltk tools utils vsn XML xtable
Packages on the GPU cluster: base bitops boot class cluster codetools datasets foreign graphics grDevices grid KernSmooth lattice MASS Matrix methods mgcv nlme nnet Rcpp rgpu rgputools rpart snow spatial splines stats stats4 survival tcltk tools utils XML (pending: RCurl Rlgi)
(you can still use install.packages() to install extra packages right now)