OptimOTU runner - redundant package installation in the script

[vmikk]

Hi!

If the pipeline runs in Docker container, are these lines required?

https://github.com/pipecraft2/pipecraft/blob/e81506fc6a1f2fb7808a4209005411ea54e4c68b/src/pipecraft-core/service_scripts/run_optimotu.sh#L48C1-L58C2

R --vanilla -e '
  # Remove existing qs2 if present
  if("qs2" %in% installed.packages()[,"Package"]) remove.packages("qs2")
  
  # Install from source with minimal optimizations
  Sys.setenv(PKG_CFLAGS="-O0 -march=x86-64")
  Sys.setenv(PKG_CXXFLAGS="-O0 -march=x86-64")
  install.packages("qs2", type="source", repos="https://cloud.r-project.org")
'

[METS0JA]

qs2 had to be installed with minimal options to properly work on macOS M series machines, In the upcoming version this installation will be only ran if the host machine is a M series macOS.