Miscellaneous

• Add custom commands and environment variables in the docker/singularity recipes automatically generated by geniac
  • Modify the conf/geniac.config file
  • Singularity
  • Docker
• How can a conda environment be activated in docker or singularity containers?
  • Properties of shells
    • Type of shells
      • Login shells
      • Interactive shells
    • Configuration files
  • Singularity
    • Example1: impossible to activate the conda environment at startup
    • Example2: activate the conda environment at startup with ‘singularity exec’ or ‘run’
    • Example3: activation of the conda environment
  • Docker
    • Example1
    • Example2
  • Application to nextflow
• Linux distributions used for the containers
• Config files for the different nextflow profiles
  • cluster
  • conda
  • docker
  • multiconda
  • multipath
  • path
  • podman
  • singularity
• Install tools from source: more examples
  • Move the tool binary in the expected folder
  • Create a bash wrapper for the tool to set required environment variables
  • Include source code from required dependencies
  • Set custom configure, build and install commands
• R with reproducible environments using renv package
  • Create a conda recipe
  • Add the label in geniac.config
  • Create a process to init the renv
  • Copy you renv.lock file is a sublder inside recipes/dependencies/
  • Add a process which uses the renv