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trust1/rbox

By trust1

•Updated over 3 years ago

Methylation array work toolbox

Image
0

136

trust1/rbox repository overview

⁠Ubuntu 20.04.2 LTS image topped with R environment // R version 4.0.3 (2020-10-10) //

⁠v1 (Meffil package upgrade to deal with EPICv2 chips)

R Environment for Methylation array data work

R libraries installed:

  • caret
  • dplyr
  • plotly
  • RANN
  • knitr
  • kableExtra
  • IlluminaHumanMethylationEPICmanifest
  • IlluminaHumanMethylationEPICanno.ilm10b4.hg19
  • RFpurify
  • LUMP
  • conumee
  • heatmaply
  • meffil
  • minfi

To make singularity container

singularity pull docker://trust1/rbox:v0

Interactive singularity session

singularity shell -B /data/MDATA:/mnt rbox_v0.sif

Non interactive singularity session

singularity exec rbox_v0.sif /usr/bin/Rscript  normalization.R
⁠Bash file for biowulf slurm

singularity_rnorm.sh

 #!/bin/sh
 #SBATCH --mem=247g
 #SBATCH --cpus-per-task=58
 #SBATCH --exclusive
 #SBATCH --gres=lscratch:100
 #SBATCH --time 24:00:00
  cd /data/MDATA/
  export TMPDIR=/lscratch/$SLURM_JOB_ID
  export SINGULARITYENV_THREADS=58
  gpfs_dirs="$(echo /gs* | tr ' ' ',')"
  export SINGULARITY_BINDPATH="/vf,${gpfs_dirs},/spin1,/data,/lscratch,/scratch,/fdb"
  module load singularity
  singularity exec rbox4_v0.sif /usr/bin/Rscript  normalization.R

To launch script

sbatch singularity_rnorm.sh

Tag summary

Content type

Image

Digest

sha256:588d1ec6a…

Size

2 GB

Last updated

over 3 years ago

docker pull trust1/rbox:v1