# R.ROSSETTA - Singularity container
https://komorowskilab.github.io/R.ROSETTA/tutorials.html#installation

## To run on Bianca
> The instructions to run anywhere else should be the same, except that when Internet is available, wine could work without installing `wine-mono`.

# Get a shell in the container environment
singularity shell /sw/apps/pm-tools/latest/rackham/singularity/R.ROSETTA/rosetta.sif

# On Bianca, Wine struggles to run without .NET which is not a problem if there is an Internet

# Run once =========
# remove any old wine installation
rm -rf ~/.wine
wine msiexec /i /opt/wine-mono-7.4.0-x86.msi

# wait until you see line like this - it will hang...
# 002c:err:winediag:nodrv_CreateWindow Make sure that your X server is running and that $DISPLAY is set correctly.
# 0040:err:setupapi:SetupDefaultQueueCallbackW copy error 1812 L"@wineusb.sys,-1" -> L"C:\\windows\\inf\\wineusb.inf"

# CTRL+C to kill the proccess - it should be ready


# One can skip the above wine-mono installation next time
# Start R from inside the container - no need to load modules!
R
...


> library(R.ROSETTA); rosetta(autcon)
...
192 1.000000e+00  3.121951    1.000000e+00     0.358:27.255
193 1.000000e+00 10.250000    9.790282e-01     1.316:79.859

$quality
 accuracyMean accuracyMedian accuracyStd accuracyMin accuracyMax
     0.804242            0.8    0.082063    0.666667    0.933333

## To run from a SBATCH script

#!/bin/bash -l
#SBATCH ...

singularity exec /sw/apps/pm-tools/latest/rackham/singularity/R.ROSETTA/rosetta.sif   Rscript program.r 

## To build the container
https://github.com/pmitev/UPPMAX-Singularity/tree/main/R.ROSETTA

# Download the definition file
wget https://github.com/pmitev/UPPMAX-Singularity/raw/main/R.ROSETTA/rosetta.def

# Build the container. On rackham run without sudo
sudo singularity build rosetta.sif rosetta.def

## Contacts:
- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425)
- [UPPMAX](https://www.uppmax.uu.se/)
- [AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ)


###### tags: `UPPMAX`