The first time you run a container with Singularity you get it cached. It takes a minute to download. From second time you run it faster, straight from cache. If the container get updated you will receive an incremental update.
List files on current directory.
singularity run docker://lbecchi/metadata:latest ls
Get NodeJS version:
singularity run docker://lbecchi/metadata:latest node -v
singularity run docker://lbecchi/metadata:latest Rscript /path/r_script_name.slurm
singularity run docker://lbecchi/metadata:latest
Job name "Rsession", 1 cores (-c1), time 1 hour (-t 1:00:00), 1 GB memory (--mem 1G)
srun --mem 1G -J RJob -c1 -t 1:00:00 singularity run docker://lbecchi/regioneR:latest Rscript /path/r_script_name.slurm parameter1 parameter2
Job name "Rsession", 4 cores (-c4), time 1 hour (-t 1:00:00), 10 GB memory (--mem 10G)
salloc --mem 10G -J RSession -c4 -t 1:00:00 singularity run docker://lbecchi/regioneR:latest
Job name "Rsession", 20 cores (-c20), time 1 hour (-t 1:00:00), 10 GB memory (--mem 10G), node name "c02" (-c02)
salloc --mem 10G -J PythonSession -c20 -w c02 -t 1:00:00 singularity exec docker://jupyter/scipy-notebook python
- r4 : R version 4.2.1 from rocker/r-ver. Brings ComplexHeatmap. Ready for testing
- regioneR : R version 4.2.1 from rocker/r-ver. Brings regioneR. Ready for testing
Dockerfile: Metadata
Packages:
- jq
- gdal/ogr
- parallel
Dockerfile: Metadata
Packages:
- Nodejs
- aternus/csv-to-xlsx
- R
- BiocManager
- minfi
- limma
- IlluminaHumanMethylation450kanno.ilmn12.hg19
- IlluminaHumanMethylationEPICanno.ilm10b4.hg19
- IlluminaHumanMethylation450kmanifest
- IlluminaHumanMethylationEPICmanifest
- data.table
- magick
- tidyverse
- vroom
- VennDiagram
- PerformanceAnalytics
- Cairo
- ComplexHeatmap
- GO.db
- corrplot