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R_singularity_README.md

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Cecret R Singularity README Stub

Purpose

Container for executing all R-based scripts and versions.sh for the CDC CLIA version of Cecret.
Prior to version 2.0, all R-based scripts and versions.sh execute within this custom Singularity container from the outside. As of version 2.0, the scripts are included in the container.

Requires

  • All
    • Singularity v.3.7.3+
  • Build
    • Cecret/configs/singularity-r.def: the Singularity definition file for the container
    • Sudo permissions on the host machine where the build is occurring (note AJW has been building on her Linux subsystem for Windows)
  • Test
    • Singularity container (*.sif) built from Cecret/configs/singularity-r.def
    • From repo: Cecret/bin/report/test_r_container.R or from container: /opt/test_r_container.R
  • Execute as a part of the Cecret pipeline
    • Singularity container (*.sif) built from Cecret/configs/singularity-r.def
    • Sequencing run ID
    • Cecret analysis directory full path on host system
    • Sequencing run directory full path on host system

Use

  • To build container
    • You must build from Cecret/configs in the cloned repo in order for the paths referenced in the def file to be valid.
    • sudo singularity build singularity-YourContainerName.sif singularity-r.def
  • To test container manually (does not require sudo)
    • singularity exec --bind /mnt,</path/to/host/directory/containing/all/files/required/for/analysis> <singularity_container_name.sif> Rscript test_r_container.R
    • Note that as of v1.1 this script is automatically run as a part of the build process (see %test section in def file).
  • To run container (does not require sudo)
    • Note
      • As of v2.0 each script is installed in the container as a separate app and must be called individually as a part of the pipeline.
      • The mount point in the host directory tree must be high enough to include all required input files and output locations below it.
    • singularity --bind /mnt,<hostMntPt> run --app orf_table <singularity_container_name.sif> <runID> <analysisDirFP>
    • singularity --bind /mnt,<hostMntPt> run --app append_tables <singularity_container_name.sif> <analysisDirFP> <file1FP> <file2FP>
    • singularity --bind /mnt,<hostMntPt> run --app report <singularity_container_name.sif> <runID> <analysisDirFP> <seqDirFP>
    • Definitions
      • = Sequencing run ID (string)
      • = Cecret output directory full path (string)
      • = Full path to sequencing run full path (string)
      • = Table file 1 with path for append_tables.R (string)
      • = Table file 2 with path for append_tables.R (string)
  • To access help files
    • Container: singularity run-help <singularity-container-name.sif>
    • Individual scripts: singularity run-help --app <appName> <singularity-container-name.sif>

Outputs

  • From build
    • singularity-container-name.sif
  • From testing
    • Print out to screen of R environment with all packages successfully loaded
  • From running